I am trying to do some SNP calling with samtools following this:
The issue is that I don't get any SNPs or indels. To check what happens, I modify this:
samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
and split it into 2 parts:
samtools mpileup -uf hg19.fa file.bam > file.tmp
and
bcftools view -bvcg file.tmp > var.raw.bcf
There is a lot of data in file.tmp, but var.raw.bcf seems too small (3k). Then, as suggested, I do:
bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
the resulting var.flt.vcf is just headers.
I guess I am missing something obvious but can't figure it now. Any ideas what I am doing wrong?
Edit: or any ideas for finding SNPs based on tophat .bam output?
The issue is that I don't get any SNPs or indels. To check what happens, I modify this:
samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
and split it into 2 parts:
samtools mpileup -uf hg19.fa file.bam > file.tmp
and
bcftools view -bvcg file.tmp > var.raw.bcf
There is a lot of data in file.tmp, but var.raw.bcf seems too small (3k). Then, as suggested, I do:
bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
the resulting var.flt.vcf is just headers.
I guess I am missing something obvious but can't figure it now. Any ideas what I am doing wrong?
Edit: or any ideas for finding SNPs based on tophat .bam output?
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