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extracting heterozygous snp from a vcf file

Dear friends,

I am very new to next gen sequencing. Using mplieup and bcftools in samtools I have generated a vcf file. I want to write a perl script to extract only the heterozygous snp. How can I understand which are heterozygous snps and how they can be extracted through a perl or any programming script.

I will be very grateful if anybody can shed some lights towards the doubt please.

Regards,

Shubhankar

next-gen snp
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updated by always_learning always_learning • written by skdutta2091 • skdutta2091

1 answer

GT tag with 0/1 is Heterozygous. You dont need to even write a script for that.

vcftools --gzvcf file.vcf.gz --extract-FORMAT-info GT | grep "0/1"

will work

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updated by Ram Ram • written by always_learning always_learning

Dear Syed, I have paired end reads. Will it work for that too?

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written by skdutta2091 • skdutta2091

It won't work if you have multiple alleles per position (you'll have genotypes like 0/2 then). I recommend using vcfbreakmulti from vcflib or LeftAlignAndTrimVariants from GATK with option --splitMultiallelics before using this script.

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updated by Ram Ram • written by mkulecka mkulecka

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