Changes

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.

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''Command to use at SeqShop Workshop:''

''Command to use at SeqShop Workshop:''

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  ${GC}/bin/vt profile_indels -g ${SS}/ref22/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 ${SS}/ref22/indel.reference.txt  -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"

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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.

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''Command to use at SeqShop Workshop:''

''Command to use at SeqShop Workshop:''

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''Command outside of SeqShop Workshop:''

''Command outside of SeqShop Workshop:''

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UMICH's algorithm for normalization has been adopted by Petr Danecek in bcftools and is also used in GKNO.

UMICH's algorithm for normalization has been adopted by Petr Danecek in bcftools and is also used in GKNO.