Assalam o Alaikum Everyone!
I have 3 annotated variants list files (excel files) of three patients from same family (2 parents 1 child). I want to extract the positions that are Hetro in parents and Homo in child.
#CHROM POS REF ALT DP AD QUAL MQ Zygosity FILTER Effect chr1 762,273 G A 39 39 1372.77 41.55 HET PASS non_coding_exon_variant chr1 866,319 G A 20 20 740.77 60.0 HOM PASS intron_variant
#CHROM POS REF ALT DP AD QUAL MQ Zygosity FILTER Effect chr1 762,109 C T 173 42 1011.77 52.75 HET PASS non_coding_exon_variant chr1 762,273 G A 35 35 1302.77 42.67 HET PASS non_coding_exon_variant
#CHROM POS REF ALT DP AD QUAL MQ Zygosity FILTER Effect chr1 762,273 G A 40 40 1457.77 40.67 HOM PASS non_coding_exon_variant chr1 866,319 G A 15 15 546.77 60.0 HOM PASS intron_variant
In the above example position 762,273 is HET in both parents and HOM in child i want to extract that whole row in a separate file. Is there any command line solution or perl script for this ??? Could anyone help ??
Thank you so much!