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# IndelRealigner/RealignerTargetCreator known site bundle files

Member
edited November 2012

Hi, For both IndelRealigner/RealignerTargetCreator, there is an option for known indel sites as below:

-known /path/to/indels.vcf


However, from the bundle files collection such as from hg19, there are several vcf files:

1000G_indels_for_realignment.hg19.vcf
1000G_omni2.5.hg19.sites.vcf
1000G_omni2.5.hg19.vcf
dbsnp_132.hg19.excluding_sites_after_129.vcf
dbsnp_132.hg19.vcf
hapmap_3.3.hg19.sites.vcf
hapmap_3.3.hg19.vcf
indels_mills_devine.hg19.sites.vcf
indels_mills_devine.hg19.vcf
NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.sites.vcf
NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.vcf


amongst them, just based on the names, 1000G_indels_for_realignment.hg19.vcf and indels_mills_devine.hg19.sites.vcf look like the files supposed to use for IndelRealigner/RealignerTargetCreator, Could you clarify the exact files for this purpose?

Since for old version, I have used 1000G_phase1.indels.hg19.vcf and Mills_and_1000G_gold_standard.indels.hg19.sites.vcf. and I compared the new and old files, quite different now.

Thanks

Mike

Post edited by Geraldine_VdAuwera on
Tagged:

• Member
edited November 2012

Hi, Geraldine:

Thanks for the input! However, the article seems not updated for the new version GATK v2.0 or newer. For example, the article mentioned for realignment, we shall use:

Mills_and_1000G_gold_standard.indels.b37.sites.vcf
1000G_phase1.indels.b37.vcf (currently from the 1000 Genomes Phase I indel calls)


which is exactly what I used for the old version I described in my original comments above. But if we look at the bundle of the new version, those files are gone or at least the names somewhat changed more or less, I copied and pasted again the files in the bundle for the new version as below:

1000G_indels_for_realignment.hg19.vcf
1000G_omni2.5.hg19.sites.vcf
1000G_omni2.5.hg19.vcf
dbsnp_132.hg19.excluding_sites_after_129.vcf
dbsnp_132.hg19.vcf
hapmap_3.3.hg19.sites.vcf
hapmap_3.3.hg19.vcf
indels_mills_devine.hg19.sites.vcf
indels_mills_devine.hg19.vcf
NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.sites.vcf
NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.vcf
`

I think for realignment, I shall use 1000G_indels_for_realignment.hg19.vcf, but what about indels_mills_devine.hg19.sites.vcf or indels_mills_devine.hg19.vcf, which one to use for realignment?

Thanks again

Mike

Post edited by Geraldine_VdAuwera on
• Member

Thanks a lot for the great detailed info, Geraldine! Appreciated! Mike

• Member

Hi, Geraldine:

Sorry,. I just realized that your web page is actually the new version. Our own installation has some confusion about the new and old versions, which was caused by our installation staffs. Sorry about confusion. your web page is fine on that.

Thanks any way for the info!

Best

Mike

• USAMember

Hello Geraldine,

I happened to use "1000G_omni2.5.hg19.vcf" instead of "Mills_and_1000G_gold_standard.indels.b37.vcf" for the paramter '-known /path/to/indels.vcf' in IndelRealigner/RealignerTargetCreator step. (I wasn't sure of the purpose of each of the vcf files in the bundle then.)

Would this be something that I should re-run with the recommended file "Mills_and_1000G_gold_standard.indels.b37.vcf".

Thanks.

@Seq2Find
Hi,

Yes, you should rerun with the recommended file. The Omni file contains SNPs only, not indels.

-Sheila

• USAMember

Thank you very much Sheila.

• Beijing Institute of Genomics, CASMember

Hi,
I read in suplementary information of 1000G main paper (2015) that they utilized in indel realignment:

ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.indels.sites.vcf.gz
ALL.wgs.low_coverage_vqsr.20101123.indels.sites.vcf.gz

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_mapping_resources/

In GATK pipeline, we have:
Mills_and_1000G_gold_standard.indels.b37.vcf
Mills_and_1000G_gold_standard.indels.b37.vcf

Could you please mention here which files are more updated and useful in your opinion??

Thanks!

Have a look at our recommendations here.

-Sheila

• Beijing Institute of Genomics, CASMember

@Sheila

Hi,
I knew the recommendations mentioned there for GATK.

do you have any idea about comparisons between these two sets of indels:

ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.indels.sites.vcf.gz (1000G pipeline)
ALL.wgs.low_coverage_vqsr.20101123.indels.sites.vcf.gz (1000G pipeline)
at
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_mapping_resources/

and
Mills_and_1000G_gold_standard.indels.b37.vcf (GATK Pipeline)
1000G_phase1.indels.b37.vcf (GATK pipeline)

Is there any difference between these two sets of files?

Regards
sohail

Issue Number
988
State
closed
Last Updated
Assignee
Array
Milestone
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Closed By
vdauwera