Depth distribution of bcftools stats output

[jfeizhu]

Why are all [4] number of genotypes 0? Thanks!

DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%)

DP 0 1 0 0.000000 1 0.390625
DP 0 2 0 0.000000 30 11.718750
DP 0 3 0 0.000000 5 1.953125
DP 0 4 0 0.000000 4 1.562500
DP 0 5 0 0.000000 4 1.562500
DP 0 6 0 0.000000 3 1.171875
DP 0 7 0 0.000000 5 1.953125
DP 0 8 0 0.000000 1 0.390625
DP 0 9 0 0.000000 1 0.390625
DP 0 10 0 0.000000 3 1.171875
DP 0 11 0 0.000000 1 0.390625
DP 0 14 0 0.000000 4 1.562500
DP 0 15 0 0.000000 1 0.390625
DP 0 16 0 0.000000 1 0.390625
DP 0 17 0 0.000000 1 0.390625
DP 0 18 0 0.000000 1 0.390625
DP 0 19 0 0.000000 1 0.390625
DP 0 20 0 0.000000 3 1.171875
DP 0 22 0 0.000000 2 0.781250
DP 0 24 0 0.000000 1 0.390625
DP 0 28 0 0.000000 1 0.390625
DP 0 29 0 0.000000 1 0.390625
DP 0 31 0 0.000000 1 0.390625
DP 0 32 0 0.000000 1 0.390625

[mcshane]

My guess is that you have no genotypes in your VCF. Is it a sites-only VCF?

[jfeizhu]

Hi Shane,

There are genotypes in my VCF files. I tested several different VCF files and all the VCF files have GT field. But the output of bcftools stats are all 0.

Thanks!

[jfeizhu]

I just used the default command to run bcftools stats.
bcftools stats test.vcf > test.txt

The following is one example record in my VCF file.

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
1 69270 . A G 95.43 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=3.48
;MQ0=243;QD=0.38;VQSLOD=-10.2561;culprit=MQ;set=FilteredInAll GT:AD:DP:GQ:PL 1/1:202,45:250:14.98:128,15,0

[mcshane]

Ah. stats by default will only look at the site information. To delve into genotypes and per-sample information, you need to run bcftools stats -s- test.vcf.

I'll close this, but link in issue #316 to make sure this gets documented when that issue is dealt with.

[jfeizhu]

Thank you so much! 👍