Question: SNP calls all seem to have quality of zero
0
gravatar for novice
3.6 years ago by
novice950
United States
novice950 wrote:

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 • 941 views
ADD COMMENTlink written 3.6 years ago by novice950
2

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.

ADD REPLYlink written 3.6 years ago by harold.smith.tarheel4.5k

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

ADD REPLYlink written 3.6 years ago by novice950
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