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172 bytes removed
, 16:46, 16 June 2014
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| 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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− | vt profile_indels -g /net/fantasia/home/atks/ref/vt/grch37/indel.reference.txt -r /net/fantasia/home/atks/ref/vt/grch37/hs37d5.fa run/final/all.genotypes.bcf -i 22:36000000-37000000 -f "PASS" | + | vt profile_indels -g indel.reference.txt -r hs37d5.fa all.genotypes.bcf -i 22:36000000-37000000 -f "PASS" |
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| data set | | data set |
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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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− | vt profile_indels -g /net/fantasia/home/atks/ref/vt/grch37/indel.reference.txt -r /net/fantasia/home/atks/ref/vt/grch37/hs37d5.fa run/final/all.genotypes.bcf -i 22:36000000-37000000 -f "~PASS" | + | vt profile_indels -g indel.reference.txt -r hs37d5.fa all.genotypes.bcf -i 22:36000000-37000000 -f "~PASS" |
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| data set | | data set |