calculate Per variant Heterozygosity from VCF file

3.1 years ago by

Republic of Ireland

Kevin Blighe ♦ 69k wrote:

NB - this does NOT support multi-allelic records. If you have these, split them via bcftools norm -m-any

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Assuming that you're confident that your VCF is normalised and that you genuinely just want to count occurrences of heterozygous calls per line, then the following will work for either phased (0|1 or 1|0) or unphased (0/1 or 1/0) genotypes, or a mixture of these.

Here, I'm actually accessing a BCF and it's the imputed 1000 Genomes Phase III data. So, the genotypes are phased.

The gsub function in AWK conveniently returns the number of matched patterns.

paste <(bcftools view 1000Genomes.Norm.bcf |\
    awk -F"\t" 'BEGIN {print "CHR\tPOS\tID\tREF\tALT"} \
      !/^#/ {print $1"\t"$2"\t"$3"\t"$4"\t"$5}') \
    \
  <(bcftools query -f '[\t%SAMPLE=%GT]\n' 1000Genomes.Norm.bcf |\
    awk 'BEGIN {print "nHet"} {print gsub(/0\|1|1\|0|0\/1|1\/0/, "")}')

CHR POS ID  REF ALT nHet
1   10177   rs367896724 A   AC  1490
1   10235   rs540431307 T   TA  6
1   10352   rs555500075 T   TA  2025
1   10505   rs548419688 A   T   1
1   10506   rs568405545 C   G   1
1   10511   rs534229142 G   A   1
1   10539   rs537182016 C   A   3
1   10542   rs572818783 C   T   1
1   10579   rs538322974 C   A   1
1   10616   rs376342519 CCGCCGTTGCAAAGGCGCGCCG  C   35
1   10642   rs558604819 G   A   21
1   11008   rs575272151 C   G   403
1   11012   rs544419019 C   G   403
1   11063   rs561109771 T   G   15
1   13011   rs574746232 T   G   3
1   13110   rs540538026 G   A   134
1   13116   rs62635286  T   G   414
1   13118   rs200579949 A   G   414

ADD COMMENT • link modified 10 months ago • written 3.1 years ago by Kevin Blighe ♦ 69k

It worked perfectly fine.. thanks for the help.. @Kevin

ADD REPLY • link written 3.1 years ago by SOHAIL • 330

You're welcome, Sohail

ADD REPLY • link written 3.1 years ago by Kevin Blighe ♦ 69k

This is almost perfect. The problem are sites like this:

0/1:1,1:2:26:0|1:27975_T_C:39,0,26

This site gives me two heterozygous counts instead of 1, I am trying to solve it, adding to gsub something like this but is not working gsub(/^0\|1|^1\|0|^0\/1|^1\/0/,"")

Any Idea?

ADD REPLY • link written 2.1 years ago by shinken123 • 100

Hey, that will require an extra if statement. The code above is designed for multi-allelic records that are encoded as 1/2, 2/2, 1/0, etc. I do not exactly have time to edit this, so, my recommendation would be to just split your multiallelic records via bcftools norm -m-any and then run the above AWK code.

How did you produce your file?

ADD REPLY • link written 2.1 years ago by Kevin Blighe ♦ 69k

I made the SNP calling with GATK.

ADD REPLY • link written 2.1 years ago by shinken123 • 100

I am not surprised (seriously) - this is an issue that re-occurs every now and then. GATK's programs can produce VCFs in a format that is difficult to use with other scripts/programs.

ADD REPLY • link written 2.1 years ago by Kevin Blighe ♦ 69k

Yep, thats True, I this case, because my file is not phased, the solution was to use your script only with the nonphases counts. like this gsub(/0\/1|1\/0/,"").

Thank you for your script It help me a lot.

ADD REPLY • link written 2.1 years ago by shinken123 • 100

Hey! Thanks. It works fine. Just a small update to use this command with a VCF file including multiallelic sites (up to four).

paste <(awk -F"\t" 'BEGIN {print "CHR\tPOS\tREF\tALT"} !/^#/ {print $1"\t"$2"\t"$4"\t"$5}' file.vcf) \
<(awk 'BEGIN {print "nHet"} !/^#/ {print gsub(/0\|1|1\|0|0\/1|1\/0|0\|2|2\|0|0\/2|2\/0|0\|3|3\|0|0\/3|3\/0|0\|4|4\|0|0\/4|4\/0/, "")}'  file.vcf)

ADD REPLY • link modified 10 months ago • written 10 months ago by gsilvaarias • 0

Thank you. Can you show some sample output just to help users?

ADD REPLY • link written 10 months ago by Kevin Blighe ♦ 69k

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