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SNP calls all seem to have quality of zero

I used the following pipeline to call SNPs on an alignment file:

$ samtools mpileup -uf s_cerevisiae.fasta aln.sorted.bam | bcftools view -O b - > snps.bcf
$ bcftools view snps.bcf | vcfutils.pl varFilter -D 100 -Q 20 > snps.vcf

The purpose of the second step is filtering calls with more than 100 read depth and those with less than 20 mapping quality. When I look at the output VCF file, however, it seems that all the calls have 0 in the QUAL column. This is true for all the samples I called SNPs for. So I am a little bit confused– would appreciate any clarification.

snp samtools vcf
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written by novice novice

A few questions/comments:

1) What does the VCF look like before 'varFilter'? It's helpful to paste a few lines.

2) bcftools 'call' has replaced 'view', which indicates older software. You're likely to get more accurate advice using the currently available versions.

• 1 views • link
written by harold.smith.tarheel harold.smith.tarheel

Thanks, Harold! It turns out I have the new version and was just confusing the bcftools commandline.

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written by novice novice

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