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VCF with SNP- count number of 100% missing genotypes

Hey,

I am using a VCF Tools for SNPs filtering. I need to count (or extract) a variable which have 100% missing genotypes (I have multisample VCF).

In VCF I know a command --max.missing, but I can define only a max missing, without a min number.

It is important for me, because I have 1 big VCF with 8 breeds' SNP's, and I would like to get information, how many SNP's are exactly in each breeds.

Thank you in advance!

vcf snp
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by misterie misterie

4 answers

genomic loci which have 100% missing coverage (or all reference calls) would not show up in a VCF anyway

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written by Jeremy Leipzig Jeremy Leipzig

You can dump the list of SNPs which are less than 100% missing, and then --exclude that list.

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written by chrchang523 chrchang523

Which command allow me to exclude this 100% missing data?

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written by misterie misterie

Look up. I told I am extracting from multisample file each breed and it generate empty variable. In my VCF file I have many breeds. I am extracting just one, and this file contain a null variable, but other breed in the same position, SNP was detected.

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written by misterie misterie

using vcffilterjdk: http://lindenb.github.io/jvarkit/VcfFilterJdk.html

 java -jar dist/vcffilterjdk.jar -e 'return !variant.getGenotypes().stream().anyMatch(G->G.isCalled());' in.vcf
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written by Pierre Lindenbaum Pierre Lindenbaum

I can not use it on my server. I can not install new softs. Exist any other option, to get this 100% missing data, using any bash, vcftools, beagle or another?

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written by misterie misterie

I can not install new softs

you don't have to install it on the server, you can always install it just for you. (and in fact, it is installed where it's compiled... )

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written by Pierre Lindenbaum Pierre Lindenbaum

but it will be impossible to run this on my files, which are on the server. I can't download it, because its too big file :(

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written by misterie misterie 
wget -O - "http://a.c.d/path/to/file.vcf.gz" | gunzip -c |  java -jar dist/vcffilterjdk.jar -e 'return !variant.getGenotypes().stream().anyMatch(G->G.isCalled());'
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written by Pierre Lindenbaum Pierre Lindenbaum

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