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Revision as of 14:03, 19 May 2015
, 14:03, 19 May 2015→Comparison with other data sets
It is usually useful to examine the call sets against known data sets for the passed variants.
It is usually useful to examine the call sets against known data sets for the passed variants.
Currently indel.reference.txt needs absolute paths to the reference files, so update indel.reference.txt to point to the reference files.
cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt
cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt
${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"
${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"
We perform the same analysis for the failed variants again, the relatively low overlap with known data sets imply a reasonable tradeoff in sensitivity and specificity.
We perform the same analysis for the failed variants again, the relatively low overlap with known data sets imply a reasonable tradeoff in sensitivity and specificity.
${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "~PASS"
${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "~PASS"
