[GenoMax]

You need to stop at the level of the directory (not include the actual executable). We are letting the system know that the file(s) I am looking for are in this directory path.

Modified file attached.

[zillur]

[QUOTE=GenoMax;153671]This is a simple work around.

Since you are having trouble editing .bash_profile file put the PATH command in a text file (let us call the file "set_path_file") using an editor. Then when you open a new terminal do the following

$ source set_path_file

Thank you very much. Using an editor I created a text file where I set the path for bowtie2, smalls, bcftools. Then in a new terminal session I typed "$ source path command.txt" it seems working and direct me to the parent directory. But commands are not found.

Mds-MacBook-Pro:~ ZILLURRAHMAN$ type bowtie
-bash: type: bowtie: not found

I have attached the file so that you can guess my mistakes.

Best Regards
Zillur

[zillur]

Thank you very much. Now I got large data like:

gi|9626243|ref|NC_001416.1| 48491 . C <X> 0 . DP=6;I16=0,3,0,0,84,2570,0,0,87,3537,0,0,25,625,0,0;QS=1,0;MQ0F=0 PL 0,9,47
gi|9626243|ref|NC_001416.1| 48492 . G <X> 0 . DP=4;I16=0,3,0,0,73,1801,0,0,87,3537,0,0,29,635,0,0;QS=1,0;MQ0F=0 PL 0,9,42
gi|9626243|ref|NC_001416.1| 48493 . A <X> 0 . DP=4;I16=0,3,0,0,72,1910,0,0,87,3537,0,0,31,661,0,0;QS=1,0;MQ0F=0 PL 0,9,50
gi|9626243|ref|NC_001416.1| 48494 . C <X> 0 . DP=3;I16=0,3,0,0,80,2194,0,0,87,3537,0,0,31,651,0,0;QS=1,0;MQ0F=0 PL 0,9,45
gi|9626243|ref|NC_001416.1| 48495 . A <X> 0 . DP=3;I16=0,2,0,0,43,1037,0,0,45,1773,0,0,25,625,0,0;QS=1,0;MQ0F=0 PL 0,6,16
gi|9626243|ref|NC_001416.1| 48496 . G <X> 0 . DP=2;I16=0,2,0,0,65,2125,0,0,45,1773,0,0,28,634,0,0;QS=1,0;MQ0F=0 PL 0,6,37
gi|9626243|ref|NC_001416.1| 48497 . G <X> 0 . DP=2;I16=0,1,0,0,27,729,0,0,3,9,0,0,25,625,0,0;QS=1,0;MQ0F=0 PL 0,3,4
gi|9626243|ref|NC_001416.1| 48498 . T <X> 0 . DP=2;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0 PL 0,0,0
gi|9626243|ref|NC_001416.1| 48499 . T <X> 0 . DP=2;I16=0,1,0,0,33,1089,0,0,42,1764,0,0,0,0,0,0;QS=1,0;MQ0F=0 PL 0,3,33
gi|9626243|ref|NC_001416.1| 48500 . A <X> 0 . DP=1;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0 PL 0,0,0
gi|9626243|ref|NC_001416.1| 48501 . C <X> 0 . DP=1;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0 PL 0,0,0
gi|9626243|ref|NC_001416.1| 48502 . G <X> 0 . DP=1;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0 PL 0,0,0

so many of this. How can I interpret this data?

Best Regards
Zillur

[GenoMax]

What it means is you just used a data file containing alignments against lambda virus and used that to call SNP's (bcftools part). Last command will let you look at the SNP's called.

$ bcftools view eg2.raw.bcf

[zillur]

Thank you very much. I think its working now.
But what does it mean?


Mds-MacBook-Pro:reference ZILLURRAHMAN$ samtools mpileup -uf lambda_virus.fa eg2.sorted.bam | bcftools view -O u - > eg2.raw.bcf
[fai_load] build FASTA index.
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
Mds-MacBook-Pro:reference ZILLURRAHMAN$ ls
commands lambda_virus.3.bt2 lambdaout.3.bt2
eg2.bam lambda_virus.4.bt2 lambdaout.4.bt2
eg2.raw.bcf lambda_virus.fa lambdaout.rev.1.bt2
eg2.sam lambda_virus.fa.fai lambdaout.rev.2.bt2
eg2.sorted.bam lambda_virus.rev.1.bt2 nohup.out
egl.sam lambda_virus.rev.2.bt2 out
lambda_virus.1.bt2 lambdaout.1.bt2 out.sam
lambda_virus.2.bt2 lambdaout.2.bt2
Mds-MacBook-Pro:reference ZILLURRAHMAN$ more lambda_virus.fa.fai
gi|9626243|ref|NC_001416.1| 48502 74 70 71
Mds-MacBook-Pro:reference ZILLURRAHMAN$ head lambda_virus.fa.fai
gi|9626243|ref|NC_001416.1| 48502 74 70 71
Mds-MacBook-Pro:reference ZILLURRAHMAN$

[GenoMax]

The command should be (I was going off what you had in your prior post)

$ samtools mpileup -uf $BT2_HOME/example/reference/lambda_virus.fa eg2.sorted.bam | bcftools view -O u - > eg2.raw.bcf

[zillur]

Thank you very much for your patience.

Mds-MacBook-Pro:reference ZILLURRAHMAN$ samtools mpileup -uf /example/reference/lambda_virus.fa eg2.sorted.bam | bcftools view -O u - > eg2.raw.bcf
[fai_load] build FASTA index.
[fai_build] fail to open the FASTA file /example/reference/lambda_virus.fa
[fai_load] fail to open FASTA index.
[vcf.c:1224 vcf_hdr_read] Could not read the header
Failed to open or the file not indexed: -
Mds-MacBook-Pro:reference ZILLURRAHMAN$ ls
commands lambda_virus.3.bt2 lambdaout.4.bt2
eg2.bam lambda_virus.4.bt2 lambdaout.rev.1.bt2
eg2.raw.bcf lambda_virus.fa lambdaout.rev.2.bt2
eg2.sam lambda_virus.rev.1.bt2 nohup.out
eg2.sorted.bam lambda_virus.rev.2.bt2 out
egl.sam lambdaout.1.bt2 out.sam
lambda_virus.1.bt2 lambdaout.2.bt2
lambda_virus.2.bt2 lambdaout.3.bt2
Mds-MacBook-Pro:reference ZILLURRAHMAN$

May be I am missing some points.

[GenoMax]

This should work.

$ samtools mpileup -uf /example/reference/lambda_virus.fa eg2.sorted.bam | bcftools view -O u  - > eg2.raw.bcf

[zillur]

Thank you very much.

Mds-MacBook-Pro:reference ZILLURRAHMAN$ ls
commands lambda_virus.3.bt2 lambdaout.4.bt2
eg2.bam lambda_virus.4.bt2 lambdaout.rev.1.bt2
eg2.raw.bcf lambda_virus.fa lambdaout.rev.2.bt2
eg2.sam lambda_virus.rev.1.bt2 nohup.out
eg2.sorted.bam lambda_virus.rev.2.bt2 out
egl.sam lambdaout.1.bt2 out.sam
lambda_virus.1.bt2 lambdaout.2.bt2
lambda_virus.2.bt2 lambdaout.3.bt2
Mds-MacBook-Pro:reference ZILLURRAHMAN$ samtools mpileup -uf /example/reference/lambda_virus.fa eg2.sorted.bam | bcftools view -O u -v -c 5 -g hom - > eg2.raw.bcf
[fai_load] build FASTA index.
[fai_build] fail to open the FASTA file /example/reference/lambda_virus.fa
[fai_load] fail to open FASTA index.
[E::hts_open] fail to open file '5'
Failed to open or the file not indexed: 5
Mds-MacBook-Pro:reference ZILLURRAHMAN$

Which thing I am missing?

Best Regards
Zillur

[GenoMax]

The command line you are using refers to the older version of bcftools (v.0.1.19). The -b option is deprecated in new bcftools (v.1.1), which you are using.

I have not tested the following command line. See if it works for you.

$ samtools mpileup -uf /example/reference/lambda_virus.fa eg2.sorted.bam | bcftools view -O u -v -c 5 -g hom - > eg2.raw.bcf

PS: If you type

$ bcftools view

Then that should print the help for the bcftools view command. You can then choose the appropriate command line options for various parameters.

[zillur]

Thank you very much. Its working now. But......


Mds-MacBook-Pro:bcftools-1.1 ZILLURRAHMAN$ export PATH="/Users/ZILLURRAHMAN/Desktop/Bioinformatics/bcftools-1.1/:$PATH"
Mds-MacBook-Pro:bcftools-1.1 ZILLURRAHMAN$ type bcftools
bcftools is /Users/ZILLURRAHMAN/Desktop/Bioinformatics/bcftools-1.1/bcftools
Mds-MacBook-Pro:bcftools-1.1 ZILLURRAHMAN$ cd ..
Mds-MacBook-Pro:bioinformatics ZILLURRAHMAN$ cd bow-tie/bowtie2-2.2.3/example/reference/
Mds-MacBook-Pro:reference ZILLURRAHMAN$ ls
commands lambda_virus.3.bt2 lambdaout.4.bt2
eg2.bam lambda_virus.4.bt2 lambdaout.rev.1.bt2
eg2.raw.bcf lambda_virus.fa lambdaout.rev.2.bt2
eg2.sam lambda_virus.rev.1.bt2 nohup.out
eg2.sorted.bam lambda_virus.rev.2.bt2 out
egl.sam lambdaout.1.bt2 out.sam
lambda_virus.1.bt2 lambdaout.2.bt2
lambda_virus.2.bt2 lambdaout.3.bt2
Mds-MacBook-Pro:reference ZILLURRAHMAN$ samtools mpileup -uf /example/reference/lambda_virus.fa eg2.sorted.bam | bcftools view -bvcg - > eg2.raw.bcf
bcftools: invalid option -- b

About: VCF/BCF conversion, view, subset and filter VCF/BCF files.
Usage: bcftools view [options] <in.vcf.gz> [region1 [...]]

Output options:
-G, --drop-genotypes drop individual genotype information (after subsetting if -s option set)
-h/H, --header-only/--no-header print the header only/suppress the header in VCF output
-l, --compression-level [0-9] compression level: 0 uncompressed, 1 best speed, 9 best compression [-1]
-o, --output-file <file> output file name [stdout]
-O, --output-type <b|u|z|v> b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]
-r, --regions <region> restrict to comma-separated list of regions
-R, --regions-file <file> restrict to regions listed in a file
-t, --targets [^]<region> similar to -r but streams rather than index-jumps. Exclude regions with "^" prefix
-T, --targets-file [^]<file> similar to -R but streams rather than index-jumps. Exclude regions with "^" prefix

Subset options:
-a, --trim-alt-alleles trim alternate alleles not seen in the subset
-I, --no-update do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
-s, --samples [^]<list> comma separated list of samples to include (or exclude with "^" prefix)
-S, --samples-file [^]<file> file of samples to include (or exclude with "^" prefix)
--force-samples only warn about unknown subset samples

Filter options:
-c/C, --min-ac/--max-ac <int>[:<type>] minimum/maximum count for non-reference (nref), 1st alternate (alt1) or minor (minor) alleles [nref]
-f, --apply-filters <list> require at least one of the listed FILTER strings (e.g. "PASS,.")
-g, --genotype [^]<hom|het|miss> require one or more hom/het/missing genotype or, if prefixed with "^", exclude sites with hom/het/missing genotypes
-i/e, --include/--exclude <expr> select/exclude sites for which the expression is true (see man page for details)
-k/n, --known/--novel select known/novel sites only (ID is not/is '.')
-m/M, --min-alleles/--max-alleles <int> minimum/maximum number of alleles listed in REF and ALT (e.g. -m2 -M2 for biallelic sites)
-p/P, --phased/--exclude-phased select/exclude sites where all samples are phased
-q/Q, --min-af/--max-af <float>[:<type>] minimum/maximum frequency for non-reference (nref), 1st alternate (alt1) or minor (minor) alleles [nref]
-u/U, --uncalled/--exclude-uncalled select/exclude sites without a called genotype
-v/V, --types/--exclude-types <list> select/exclude comma-separated list of variant types: snps,indels,mnps,other [null]
-x/X, --private/--exclude-private select/exclude sites where the non-reference alleles are exclusive (private) to the subset samples

[fai_load] build FASTA index.
[fai_build] fail to open the FASTA file /example/reference/lambda_virus.fa
[fai_load] fail to open FASTA index.
Mds-MacBook-Pro:reference ZILLURRAHMAN$ ls
commands lambda_virus.3.bt2 lambdaout.4.bt2
eg2.bam lambda_virus.4.bt2 lambdaout.rev.1.bt2
eg2.raw.bcf lambda_virus.fa lambdaout.rev.2.bt2
eg2.sam lambda_virus.rev.1.bt2 nohup.out
eg2.sorted.bam lambda_virus.rev.2.bt2 out
egl.sam lambdaout.1.bt2 out.sam
lambda_virus.1.bt2 lambdaout.2.bt2
lambda_virus.2.bt2 lambdaout.3.bt2
Mds-MacBook-Pro:reference ZILLURRAHMAN$ samtools mpileup -uf /lambda_virus.fa eg2.sorted.bam | bcftools view -bvcg - > eg2.raw.bcf
bcftools: invalid option -- b

About: VCF/BCF conversion, view, subset and filter VCF/BCF files.
Usage: bcftools view [options] <in.vcf.gz> [region1 [...]]

Output options:
-G, --drop-genotypes drop individual genotype information (after subsetting if -s option set)
-h/H, --header-only/--no-header print the header only/suppress the header in VCF output
-l, --compression-level [0-9] compression level: 0 uncompressed, 1 best speed, 9 best compression [-1]
-o, --output-file <file> output file name [stdout]
-O, --output-type <b|u|z|v> b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]
-r, --regions <region> restrict to comma-separated list of regions
-R, --regions-file <file> restrict to regions listed in a file
-t, --targets [^]<region> similar to -r but streams rather than index-jumps. Exclude regions with "^" prefix
-T, --targets-file [^]<file> similar to -R but streams rather than index-jumps. Exclude regions with "^" prefix

Subset options:
-a, --trim-alt-alleles trim alternate alleles not seen in the subset
-I, --no-update do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
-s, --samples [^]<list> comma separated list of samples to include (or exclude with "^" prefix)
-S, --samples-file [^]<file> file of samples to include (or exclude with "^" prefix)
--force-samples only warn about unknown subset samples

Filter options:
-c/C, --min-ac/--max-ac <int>[:<type>] minimum/maximum count for non-reference (nref), 1st alternate (alt1) or minor (minor) alleles [nref]
-f, --apply-filters <list> require at least one of the listed FILTER strings (e.g. "PASS,.")
-g, --genotype [^]<hom|het|miss> require one or more hom/het/missing genotype or, if prefixed with "^", exclude sites with hom/het/missing genotypes
-i/e, --include/--exclude <expr> select/exclude sites for which the expression is true (see man page for details)
-k/n, --known/--novel select known/novel sites only (ID is not/is '.')
-m/M, --min-alleles/--max-alleles <int> minimum/maximum number of alleles listed in REF and ALT (e.g. -m2 -M2 for biallelic sites)
-p/P, --phased/--exclude-phased select/exclude sites where all samples are phased
-q/Q, --min-af/--max-af <float>[:<type>] minimum/maximum frequency for non-reference (nref), 1st alternate (alt1) or minor (minor) alleles [nref]
-u/U, --uncalled/--exclude-uncalled select/exclude sites without a called genotype
-v/V, --types/--exclude-types <list> select/exclude comma-separated list of variant types: snps,indels,mnps,other [null]
-x/X, --private/--exclude-private select/exclude sites where the non-reference alleles are exclusive (private) to the subset samples

[fai_load] build FASTA index.
[fai_build] fail to open the FASTA file /lambda_virus.fa
[fai_load] fail to open FASTA index.
Mds-MacBook-Pro:reference ZILLURRAHMAN$ ls
commands lambda_virus.3.bt2 lambdaout.4.bt2
eg2.bam lambda_virus.4.bt2 lambdaout.rev.1.bt2
eg2.raw.bcf lambda_virus.fa lambdaout.rev.2.bt2
eg2.sam lambda_virus.rev.1.bt2 nohup.out
eg2.sorted.bam lambda_virus.rev.2.bt2 out
egl.sam lambdaout.1.bt2 out.sam
lambda_virus.1.bt2 lambdaout.2.bt2
lambda_virus.2.bt2 lambdaout.3.bt2
Mds-MacBook-Pro:reference ZILLURRAHMAN$ samtools mpileup -uf /reference/lambda_virus.fa eg2.sorted.bam | bcftools view -bvcg - > eg2.raw.bcf
bcftools: invalid option -- b

About: VCF/BCF conversion, view, subset and filter VCF/BCF files.
Usage: bcftools view [options] <in.vcf.gz> [region1 [...]]

Output options:
-G, --drop-genotypes drop individual genotype information (after subsetting if -s option set)
-h/H, --header-only/--no-header print the header only/suppress the header in VCF output
-l, --compression-level [0-9] compression level: 0 uncompressed, 1 best speed, 9 best compression [-1]
-o, --output-file <file> output file name [stdout]
-O, --output-type <b|u|z|v> b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]
-r, --regions <region> restrict to comma-separated list of regions
-R, --regions-file <file> restrict to regions listed in a file
-t, --targets [^]<region> similar to -r but streams rather than index-jumps. Exclude regions with "^" prefix
-T, --targets-file [^]<file> similar to -R but streams rather than index-jumps. Exclude regions with "^" prefix

Subset options:
-a, --trim-alt-alleles trim alternate alleles not seen in the subset
-I, --no-update do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
-s, --samples [^]<list> comma separated list of samples to include (or exclude with "^" prefix)
-S, --samples-file [^]<file> file of samples to include (or exclude with "^" prefix)
--force-samples only warn about unknown subset samples

Filter options:
-c/C, --min-ac/--max-ac <int>[:<type>] minimum/maximum count for non-reference (nref), 1st alternate (alt1) or minor (minor) alleles [nref]
-f, --apply-filters <list> require at least one of the listed FILTER strings (e.g. "PASS,.")
-g, --genotype [^]<hom|het|miss> require one or more hom/het/missing genotype or, if prefixed with "^", exclude sites with hom/het/missing genotypes
-i/e, --include/--exclude <expr> select/exclude sites for which the expression is true (see man page for details)
-k/n, --known/--novel select known/novel sites only (ID is not/is '.')
-m/M, --min-alleles/--max-alleles <int> minimum/maximum number of alleles listed in REF and ALT (e.g. -m2 -M2 for biallelic sites)
-p/P, --phased/--exclude-phased select/exclude sites where all samples are phased
-q/Q, --min-af/--max-af <float>[:<type>] minimum/maximum frequency for non-reference (nref), 1st alternate (alt1) or minor (minor) alleles [nref]
-u/U, --uncalled/--exclude-uncalled select/exclude sites without a called genotype
-v/V, --types/--exclude-types <list> select/exclude comma-separated list of variant types: snps,indels,mnps,other [null]
-x/X, --private/--exclude-private select/exclude sites where the non-reference alleles are exclusive (private) to the subset samples

[fai_load] build FASTA index.
[fai_build] fail to open the FASTA file /reference/lambda_virus.fa
[fai_load] fail to open FASTA index.
Mds-MacBook-Pro:reference ZILLURRAHMAN$ ls
commands lambda_virus.3.bt2 lambdaout.4.bt2
eg2.bam lambda_virus.4.bt2 lambdaout.rev.1.bt2
eg2.raw.bcf lambda_virus.fa lambdaout.rev.2.bt2
eg2.sam lambda_virus.rev.1.bt2 nohup.out
eg2.sorted.bam lambda_virus.rev.2.bt2 out
egl.sam lambdaout.1.bt2 out.sam
lambda_virus.1.bt2 lambdaout.2.bt2
lambda_virus.2.bt2 lambdaout.3.bt2
Mds-MacBook-Pro:reference ZILLURRAHMAN$

[fai_load] build FASTA index.
[fai_build] fail to open the FASTA file /reference/lambda_virus.fa
[fai_load] fail to open FASTA index.

What does it mean?

Best Regards
Zillur

[GenoMax]

You added an extra bcftools word at the end of your path command. Command should be

$ export PATH="/Users/ZILLURRAHMAN/Desktop/Bioinformatics/bcftools-1.1:$PATH"

[zillur]

Thank you very much. May be I am missing something. Still bcftools command can't be found.

Mds-MacBook-Pro:bcftools-1.1 ZILLURRAHMAN$ chmod u+x /Users/ZILLURRAHMAN/Desktop/Bioinformatics/bcftools-1.1/bcftools/bcftools
chmod: /Users/ZILLURRAHMAN/Desktop/Bioinformatics/bcftools-1.1/bcftools/bcftools: Not a directory
Mds-MacBook-Pro:bcftools-1.1 ZILLURRAHMAN$ chmod u+x /Users/ZILLURRAHMAN/Desktop/Bioinformatics/bcftools-1.1/bcftools
Mds-MacBook-Pro:bcftools-1.1 ZILLURRAHMAN$ type bcftools
-bash: type: bcftools: not found
Mds-MacBook-Pro:bcftools-1.1 ZILLURRAHMAN$ export PATH="/Users/ZILLURRAHMAN/Desktop/Bioinformatics/bcftools-1.1/bcftools/:$PATH"
Mds-MacBook-Pro:bcftools-1.1 ZILLURRAHMAN$ type bcftools
-bash: type: bcftools: not found
Mds-MacBook-Pro:bcftools-1.1 ZILLURRAHMAN$

[GenoMax]

You need to add execute permissions to the new bcftools executable.

$ chmod u+x /Users/ZILLURRAHMAN/Desktop/Bioinformatics/bcftools-1.1/bcftools/bcftools

[zillur]

Thank you very much. I downloaded and compiled it using "make" command. Then tried to create path for "bcftools" using previous trick but it is not working here.

Mds-MacBook-Pro:bioinformatics ZILLURRAHMAN$ cd bcftools-1.1/
Mds-MacBook-Pro:bcftools-1.1 ZILLURRAHMAN$ ls
AUTHORS em.c prob1.c vcfconcat.c vcfquery.c
HMM.c em.o prob1.h vcfconcat.o vcfquery.o
HMM.h filter.c prob1.o vcfconvert.c vcfroh.c
HMM.o filter.h rbuf.h vcfconvert.o vcfroh.o
INSTALL filter.o reheader.c vcffilter.c vcfsom.c
LICENSE gvcf.c reheader.o vcffilter.o vcfsom.o
Makefile gvcf.o tabix.c vcfgtcheck.c vcfstats.c
README htslib-1.1 tabix.o vcfgtcheck.o vcfstats.o
bcftools khash_str2str.h test vcfindex.c vcfutils.pl
bcftools.1 kmin.c tsv2vcf.c vcfindex.o vcfview.c
bcftools.h kmin.h tsv2vcf.h vcfisec.c vcfview.o
bcftools.txt kmin.o tsv2vcf.o vcfisec.o vcmp.c
call.h main.c vcfannotate.c vcfmerge.c vcmp.h
ccall.c main.o vcfannotate.o vcfmerge.o vcmp.o
ccall.o mcall.c vcfcall.c vcfnorm.c version.c
convert.c mcall.o vcfcall.o vcfnorm.o version.h
convert.h plot-vcfstats vcfcnv.c vcfplugin.c
convert.o plugins vcfcnv.o vcfplugin.o
Mds-MacBook-Pro:bcftools-1.1 ZILLURRAHMAN$ pwd
/Users/ZILLURRAHMAN/desktop/bioinformatics/bcftools-1.1
Mds-MacBook-Pro:bcftools-1.1 ZILLURRAHMAN$ export PATH="/Users/ZILLURRAHMAN/Desktop/Bioinformatics/bcftools-1.1/bcftools/:$PATH"
Mds-MacBook-Pro:bcftools-1.1 ZILLURRAHMAN$ type bcftools
-bash: type: bcftools: not found
Mds-MacBook-Pro:bcftools-1.1 ZILLURRAHMAN$

Would you please to tell me which point I missed?

Best regards
Zillur