Question: Need help teasing out insertions and deletions with bcftools stats file.vcf > file.stats
gravatar for oars
2.7 years ago by
oars160 wrote:

The following is a neat feature found in bcftools...

bcftools stats file.vcf > file.stats

...however, it doesn't seem to differentiate between insertions or deletions - just indels?

Here is an example of the output:

# SN    [2]id   [3]key  [4]value
SN  0   number of samples:  1
SN  0   number of records:  1761
SN  0   number of no-ALTs:  0
SN  0   number of SNPs: 1663
SN  0   number of MNPs: 0
SN  0   number of indels:   98
SN  0   number of others:   0
SN  0   number of multiallelic sites:   2
SN  0   number of multiallelic SNP sites:   0
# TSTV, transitions/transversions:
# TSTV  [2]id   [3]ts   [4]tv   [5]ts/tv    [6]ts (1st ALT) [7]tv (1st ALT) [8]ts/tv (1st ALT)
TSTV    0   1267    396 3.20    1267    396 3.20

Is there a way to separate the insertions and deletions using bcftools?

Pie in the sky would be a stats read out option that would also provide information about heterozygous genotypes and dbSNP sites.

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by oars160

is there a SVTYPE tag in the INFO column ?

ADD REPLYlink written 2.7 years ago by Pierre Lindenbaum131k

I don't think so, I see the following...

AC=1;AF=0.500;AN=2;BaseQRankSum=-1.483;ClippingRankSum=0.000;DP=75;ExcessHet=3.0103;FS=2.014;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=14.48;ReadPosRankSum=1.552;SOR=1.047   GT:AD:DP:GQ:PL  0/1:40,34:74:99:1100,0,1414
ADD REPLYlink written 2.7 years ago by oars160

I've also tried vcftools with its vcf-stats feature:

vcf-stats file.vcf

This also provides an indel count but does not separate insertions and deletions, it does however provide a confusing list following the indel count. I'm not sure what it represents and its not clear from the manual pages.

However, this simple command line vcftools script from matt (Count Of Variants) seems to do the trick:

$ zcat SRR1611183.gatk.vcf.gz | vcf-annotate --fill-type | grep -oP "TYPE=\w+" | sort | uniq -c
     56 TYPE=del
     42 TYPE=ins
   1663 TYPE=snp
ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by oars160
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