[kurban910]

Is the bcftools executable in the directory you are currently in? Have you tried to "locate" it and provide the full path for it like you did for vcfutils.pl?

Is your my.var.bcf file in the current directory?

In future, start a new thread when you have a new question.

1. bcftools is executable in my current directory.

kurban@kurban-X550VC:~/Desktop/SNPs/CD$ bcftools

Program: bcftools (Tools for data in the VCF/BCF formats)
Version: 0.1.17-dev (r973:277)

Usage: bcftools <command> <arguments>

Command: view print, extract, convert and call SNPs from BCF
index index BCF
cat concatenate BCFs
ld compute all-pair r^2
ldpair compute r^2 between requested pairs


2.i have tried to provide full path of bcftools:
kurban@kurban-X550VC:~/Desktop/SNPs/CD$ /usr/bin/bcftools view my.var.bcf | /usr/share/samtools/vcfutils.pl varFilter - > my.var-final.vcf
it says:
open: No such file or directory
and file my.var.bcf is in my current diractory.

but it is still not working.

[GenoMax]

Are you sure bcftools in in your current directory (~/Desktop/SNPs/CD from what I can see above)? You seem to be running the copy that is in /usr/bin (in the set of commands in #2).

Have you verified that my.var.bcf file is non-zero bytes (i.e. there is something in it)?

Can you use [ CODE] (remove the leading space before CODE) put your commands here [/CODE] to make the commands you are pasting clear (enclose them in CODE tags on both sides like I have shown). Otherwise it is difficult to decipher if there are spaces in wrong spot in your command line.

[blakeoft]

kurban910, I just ran

bcftools view jim.bcf

and I don't have any file called jim.bcf. It gave me this:

open: No such file or directory

This makes me think that you have the wrong name. Be careful with 1's and l's, -'s and _'s, etc -- it's easy to get these confused. Heck, I even get .'s and _'s confused sometimes. In the directory that the bcf file is located, can you execute:

ls $PWD/*.bcf

and copy the bcf file's name exactly as it appears, including the full path, and then try running your command again?

[kurban910]

kurban910, are you sure that you have the right name for the bcf file? It looks to me like the command is correct.

yes, i am sure the file name is right

[kurban910]

Are you sure bcftools in in your current directory (~/Desktop/SNPs/CD from what I can see above)? You seem to be running the copy that is in /usr/bin (in the set of commands in #2).

Have you verified that my.var.bcf file is non-zero bytes (i.e. there is something in it)?

Can you use [ CODE] (remove the leading space before CODE) put your commands here [/CODE] to make the commands you are pasting clear (enclose them in CODE tags on both sides like I have shown). Otherwise it is difficult to decipher if there are spaces in wrong spot in your command line.

u r right ,thanks. i will put the commends in the code box next time. and yes, my.var.bcf file is around 7.6 BM.

and for your first question, bcftools is not in the current directory i am in, but its executable from here.

[kurban910]

kurban910, I just ran

bcftools view jim.bcf

and I don't have any file called jim.bcf. It gave me this:

open: No such file or directory

This makes me think that you have the wrong name. Be careful with 1's and l's, -'s and _'s, etc -- it's easy to get these confused. Heck, I even get .'s and _'s confused sometimes. In the directory that the bcf file is located, can you execute:

ls $PWD/*.bcf

and copy the bcf file's name exactly as it appears, including the full path, and then try running your command again?

thank you for your time guys , now i find out not just this one, other commends also r not exacted in my terminal , ubuntu 12.04 some times isn’t stable . after i reinstall the system i will try again.

[maubp]

If you did want to convert the FASTQ to an unaligned SAM or BAM file, try this:
http://picard.sourceforge.net/comman...tml#FastqToSam

I need to do this locally, and since we didn't have Picard installed but do have Biopython (yes, I'm biased ), I wrote a simple Python script to convert paired FASTQ files into unmapped SAM reads (which you can pipe into samtools to get as a BAM file):

https://github.com/peterjc/picobio/blob/master/sambam/fastq_to_sam.py

I would expect this to be slower than a dedicated tool, so probably not suitable for a high throughput pipeline - but it should be fine for a one-off analysis.