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Revision as of 15:29, 26 June 2014
, 15:29, 26 June 2014→Normalization
- about a loss of 11% of variant thought distinct.
- about a loss of 11% of variant thought distinct.
For chromosome 22, there are 121 variants, but only 106 distinct Indels after normalization
- about a loss of 12% of variant thought distinct.
To normalize and remove duplicate variants for chromosome 22:
${GC}/bin/vt normalize ${SS}/ref22/mills_indels_hg19.22.sites.bcf -r ${SS}/ref22/human.g1k.v37.chr22.fa | ${GC}/bin/vt mergedups - -o ${OUT}/mills.22.normalized.genotypes.bcf
and you will observe that 43 variants had to be left aligned and 15 variants were removed.
<pre>
stats: biallelic
no. left trimmed : 0
no. left trimmed : 0
no. left trimmed and left aligned : 0
no. left trimmed and left aligned : 0
no. left trimmed and right trimmed : 0
no. left trimmed and right trimmed : 0
no. left aligned : 3994
no. left aligned : 43
no. right trimmed : 0 <br>
no. right trimmed : 0
total no. biallelic normalized : 43
multiallelic
no. left trimmed : 0
no. left trimmed : 0
no. left trimmed and left aligned : 0
no. left trimmed and left aligned : 0
no. left trimmed and right trimmed : 0
no. left trimmed and right trimmed : 0
no. left aligned : 0
no. left aligned : 0
no. right trimmed : 0 <br>
no. right trimmed : 0
no. variants observed : 9996 <br>
total no. multiallelic normalized : 0
total no. variants normalized : 43
total no. variants observed : 121
stats: Total number of observed variants 121
Total number of unique variants 106
</pre>
Let's look for a variant that was normalized.
Let's look at the last two variants that were normalized.
${GC}/bin/vt view ${OUT}/mills.normalized.genotypes.bcf | grep OLD_VARIANT |head -1
${GC}/bin/vt view ${OUT}/mills.22.normalized.genotypes.bcf | grep OLD_VARIANT |tail -2
Results:
Results:
*The position has changed - it was:
*The positions have changed - the were:
** 18293100 (as seen after OLD_VARIANT)
** 48831918 & 50012616 (as seen after OLD_VARIANT)
*Now it is
*Now they are:
** 18293097
** 48831915 & 50012614
[[File:indelNormalize.png|800px]]
[[File:indelNormalize.png|800px]]
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.
