extraction homozygous SNPs for first individual when second individual has no SNPs in same position

Question

[kk.mahsa]

hi

how i can extract homozygous SNPs for first individual (vcf file) when second individual has no SNPs in the same position?

thanks in advance

Answer 1

[Pierre Lindenbaum]

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

n extract homozygous SNPs for first individual (vcf file)

I understand this as "genotype[0] is homozygous for the ALT allele and genotype[1] is Hom-Ref or is not Called"

java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotype(0).isHomVar() && (variant.getGenotype(1).isHomRef() || !variant.getGenotype(1).isCalled());' input.vcf

[kk.mahsa]

thanks for your quick answer dear Pierre, i think my question is not clear. i have two vcf file and my goal is extraction Homozygous snps for first vcf file when second vcf file has no snp (hom or het) in that position.

[Pierre Lindenbaum]

i have two vcf file and my goal is extraction Homozygous snps for first vcf file when second vcf file has no snp (hom or het)

merge the two vcfs : https://www.google.fr/search?q=merge+vcf+site%3Abiostars.org

and the filter with my command above.

[kk.mahsa]

i installed your program but there is not vcffilterjdk.jar file in dist folder. thare are three files including: vcffilterjs.jar, annotproc.jar and vcffilterjs.

so i try:

vcf-merge input_1.vcf input_2.vcf > merged.vcf

java -jar dist/vcffilterjs.jar -e 'return variant.getGenotype(0).isHomVar() && (variant.getGenotype(1).isHomRef() || !variant.getGenotype(1).isCalled());' merged.vcf

and get this error (https://ufile.io/h94hj)