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Revision as of 14:37, 26 June 2014
, 14:37, 26 June 2014→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.
${GC}/bin/vt profile_indels -g ${VTREF}/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"
In order to do this, you need to update indel.reference.txt to point to the reference files.
cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt
Edit indel.reference.txt and specify the correct path to ${SS}
nedit ${OUT}/indel.reference.txt
${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/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 ${VTREF}/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/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}/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "~PASS"
data set
data set
