at first, I install samtools by ubuntu software center. samtools of old version.
when i command 'samtools pileup -vcf ref.fasta aln.sorted.bam > aln_result'
then samtools make aln_result file and it shows the raw indel/snp information which is not corresponding reference.
i reinstalled ubuntu and i installed samtools by downloading from sourceforge.net(latest version)
as you know, 'pileup' option is deprecated and replaced with 'mpileup' option.
I just followed 'Manual Reference Pages - samtools', my command line is like this;
samtools mpileup -C50 -gf ref.fasta aln.sorted.bam > file1(it's compressed binary file)
bcftools index file1
bcftools view file1 chr*:****-**** > out.vcf
bcftools view -vc file1 > out.vcf 2 > out.afs
I couldn't open file1 because it's binary format and out.vcf shows snp/indel but cannot recognize ref.fasta so only dot('.') is shown at the REF column.
where am i wrong?(reference file is absolutely normal as i know. when i use tview option, the reference sequence is shown well)
is it right to input file1 to in.bcf at using bcftools?
when i command 'samtools pileup -vcf ref.fasta aln.sorted.bam > aln_result'
then samtools make aln_result file and it shows the raw indel/snp information which is not corresponding reference.
i reinstalled ubuntu and i installed samtools by downloading from sourceforge.net(latest version)
as you know, 'pileup' option is deprecated and replaced with 'mpileup' option.
I just followed 'Manual Reference Pages - samtools', my command line is like this;
samtools mpileup -C50 -gf ref.fasta aln.sorted.bam > file1(it's compressed binary file)
bcftools index file1
bcftools view file1 chr*:****-**** > out.vcf
bcftools view -vc file1 > out.vcf 2 > out.afs
I couldn't open file1 because it's binary format and out.vcf shows snp/indel but cannot recognize ref.fasta so only dot('.') is shown at the REF column.
where am i wrong?(reference file is absolutely normal as i know. when i use tview option, the reference sequence is shown well)
is it right to input file1 to in.bcf at using bcftools?
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