3,045
edits
Changes
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Revision as of 13:52, 17 June 2014
, 13:52, 17 June 2014→Normalization
To normalize and remove duplicate variants:
To normalize and remove duplicate variants:
${GC}/bin/vt normalize mills.genotypes.bcf -r hs37d5.fa | ${GC}/bin/vt mergedups - -o mills.normalized.genotypes.bcf
${GC}/bin/vt normalize ${VTREF}/mills_indels_hg19.sites.bcf -r ${VTREF}/hs37d5.fa | ${GC}/bin/vt mergedups - -o ${OUT}/mills.normalized.genotypes.bcf
and you will observe that 3994 variants had to be left aligned and 1092 variants were removed.
and you will observe that 3994 variants had to be left aligned and 1092 variants were removed.
Total number of unique variants 8904 <br>
Total number of unique variants 8904 <br>
Let's look for a variant that was normalized.
${GC}/bin/vt view ${OUT}/mills.normalized.genotypes.bcf | grep OLD_VARIANT |head -1
Results:
1 18293097 . T TCTC . PASS VC=INDEL;AC=263;AF=0.84;AN=314;OLD_VARIANT=1:18293100:C/CCTC
The position has changed - it was:
* 18293100 (as seen after OLD_VARIANT)
Now it is
* 18293097
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.
