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== Comparisons ==
== Comparisons ==
=== 20 May 2014 ===
The following table shows the number of variants normalized for an anonymous data set. This analysis was done on 20 May 2014.
The following table shows the number of variants normalized for an anonymous data set. This analysis was done on 20 May 2014.
Issues have been communicated to bcftools and gatk developers on 20 May 2014.
Issues have been communicated to bcftools and gatk developers on 20 May 2014.
=== 22 May 2014 ===
The following table shows the number of variants normalized for an anonymous data set. This analysis was done on 22 May 2014.
bcftools was updated.
{| class="wikitable"
|-
! scope="col"| Dataset
! scope="col"| bcftools
! scope="col"| gatk
! scope="col"| vt
! scope="col"| comments
|-
| #normalized
| 18849
| 18794
| 18849
| bcftools's algorithm is the same as vt now
|-
| #normalized after bcftools
| 0
| 0
| 0
| no variants processed by bcftools were further normalized.
|-
| #normalized after gatk
| 0
| 0
| 57
| 57 variants from GATK's normalization were left aligned by vt. 6 were biallelic and 51 were multiallelic. Note that 2 variants were changed by GATK but were not completely normalized.
|-
| #normalized after vt
| 0
| 0
| 0
| no variants processed by vt were further normalized.
|}
Commands used are:
*bcftools norm -f ref.fa in.vcf -O z > out.vcf.gz
*java -jar GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants --trimAlleles -R ref.fa --variant in.vcf.gz -o out.vcf.gz
*vt normalize -r ref.vcf.gz -o out.vcf.gz
Versions are:
*bcftools v0.2.0-rc8-5-g0e06231 (using htslib 0.2.0-rc8-6-gd49dfa6) [updated non release development version]
*GATK v3.1-1-g07a4bf8
*vt normalize v0.5
= Maintained by =
= Maintained by =
This page is maintained by [mailto:atks@umich.edu Adrian].
This page is maintained by [mailto:atks@umich.edu Adrian].
