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i run VQSR on the vcf file generated by unified genotyper and filtered PASS 63412 out of 86840 (files with snps and indels). as i run unified genotyper with -glm BOTH command. i have two questions
1) the number of pass snps are different when i counted them in two ways(first with original output of UG and other by separating snps and indel into two separate files using awk script
grep -v "#" sample1_recalibrated_snps_PASS.vcf | grep -c "PASS"
grep -v "#" sample1_merged_recalibrated_snps_raw_indels.vcf| grep -c "LowQual“
Statistics for separate snp file. here i use awk script to separate snps and indels (using awk script)
Rest is fine only problem is that pass snps no differ think why
grep -v "^#" sample1_snp.vcf| grep -c "PASS
grep -v "^#" sample1_snp.vcf| grep -c "LowQual“
2) i run VQSR on snps generated by unified genotyper i need to ask query about VQSR tranche plot for Snps.
in my case tranche is not showing any false positive call see plot attached what do i interpret that there is no FP which seems surprising
when i tried to run VQSR on INDELS (in the same file) it doesnt work as i had 884 indels which i read from VQSR documentation and questions asked by ppl is small.