GATK: VCF file for Local realignment around indels

[jorge]

Hello,

I'd like to perform a 'Local realignment around indels' on bam file uisng GATK. However I'm still unclear about the vcf file with the known indels that I should provide. I'd say that the 'dbsnp_132.hg19.vcf' file included in the bundle should do as it seems to include indel data. Also, should I filter out non-indels form that file in order to speed up the realignment?

I'd be grate if someone could comment on this.

Thanks
Jorge

[raonyguimaraes]

Probably all the files you will need are avaiable at :

ftp://ftp.broadinstitute.org/bundle/1.2/hg19/

For indels you should use the file: ftp://[email protected]

Inserted with the command: -B:indels,vcf 1000G_biallelic.indels.hg19.vcf

[jorge]

Thanks a lot for the information!

Jorge