No qual scores in VCF

Question

[Jon Binkley]

I have the latest versions of htslib (1.3.2), samtools (1.3.1), and bcftools (1.3.1) installed. System is CentOS 5.

The first oddity is that bcftools mpileup does not work; it returns: unrecognized command 'mpileup'

mpileup seems to run fine with samtools. However, the resulting VCF file has all zero values in the QUAL column. The qual scores in the input BAM file look fine.

The mpileup command was:

samtools mpileup -uvf refseq.fasta -o reads.vcf reads.bam

Any advice or suggestions would be greatly appreciated!

Answer 1

[igor]

Check the example for variant calling at the samtools page: http://samtools.sourceforge.net/mpileup.shtml

They also provide the following explanation:

In the command line above, samtools collects summary information in the input BAMs, computes the likelihood of data given each possible genotype and stores the likelihoods in the BCF format (see below). It does not call variants. Bcftools applies the prior and does the actual calling. It can also concatenate BCF files, index BCFs for fast random access and convert BCF to VCF.

In your case, you are only running the samtools portion.

Answer 2

[Jon Binkley]

Thank you for the tip, igor -- works fine now.

Here is the final command line:

samtools mpileup -uvf refseq.fasta reads.bam | bcftools call -mv | bcftools filter -s LowQual -e '%QUAL<20' -O z -o reads.vcf.bz

Answer 3

[524423189]

I also have same problem which the QUAL column are all zero.

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 027-control.merge.bam

cdtA 1 . A <x> 0 . DP=53;I16=52,1,0,0, then I used "bcftools call" to call variants, but the QUAL column has two values separated by comma, like this:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 027-control.merge.bam

cdtA 1 . A . 189.996 . DP=53;MQSB=1;MQ0F=0;AF1=0;AC1=0;DP4=52,1,0,0;MQ=60;FQ=-186.988 GT:PL 0/0:0 cdtA 2 . T . 192.996 . DP=54;MQSB=1;MQ0F=0;AF1=0;AC1=0;DP4=53,1,0,0;MQ=60;FQ=-189.988 GT:PL 0/0:0

so, what's the means for these two QUALs, anyone could give some advice? Thank you.