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This group provides a forum for questions or discussion related to Genome VCF (gVCF) conventions the gvcftools utilities.

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Mark Cowley, … Saunders, Chris7

7/27/15

merge_variants behaviour for INDELs

H Dheeraj – The proposed change below was to document the issue, which looks like it went in soon

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merge_variants behaviour for INDELs

H Dheeraj – The proposed change below was to document the issue, which looks like it went in soon

7/27/15

6/26/15

--murdock option usage

Hi, I am trying to merge gVCFs produced form illumina and indel conflict error was as mentioned by

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--murdock option usage

Hi, I am trying to merge gVCFs produced form illumina and indel conflict error was as mentioned by

6/26/15

Victoria Fernandez, Saunders, Chris3

4/15/15

twins fails to load idx file

Thanks!!! after reindexing file now works!! On Wednesday, 15 April 2015 15:46:29 UTC-5, Chris

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twins fails to load idx file

Thanks!!! after reindexing file now works!! On Wednesday, 15 April 2015 15:46:29 UTC-5, Chris

4/15/15

Katherine Smith2

12/8/14

merge_variants error - multiple conflicting variants at the same position of input gVCF

OK, I've figured it out - option --murdock is required. > bgzip out.vcf > tabix -p vcf out.

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merge_variants error - multiple conflicting variants at the same position of input gVCF

OK, I've figured it out - option --murdock is required. > bgzip out.vcf > tabix -p vcf out.

12/8/14

greyson twist, Saunders, Chris5

5/28/14

Hey Chris, we have been using gvcftools for awhile now, it is a great tool that saves us lots of

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Hey Chris, we have been using gvcftools for awhile now, it is a great tool that saves us lots of

5/28/14

Vivek, Saunders, Chris2

11/28/13

VCF to gVCF conversion

Hi Vivek, I don't have any recommendations for combining large-scale variant calls into a single

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VCF to gVCF conversion

Hi Vivek, I don't have any recommendations for combining large-scale variant calls into a single

11/28/13

Wanmei Ou, Saunders, Chris2

6/14/13

To leverage multi-sample variant call

Hi Wanmei, Great question… it certainly is possible and is not gated by needing a multi-sample

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To leverage multi-sample variant call

Hi Wanmei, Great question… it certainly is possible and is not gated by needing a multi-sample

6/14/13

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