
Shirely
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Activity overview
Latest activity by Shirely-
Shirely commented,
Thanks a lot.
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Shirely commented,
Hey, Thanks for you answer. But I didn't find the argument to specify ploidy for chromosome X, and only find the --sample-ploidy argument to specify the number of the chromosome. Could you please ...
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Shirely created a post,
why I have a 1/1 genotype on chromosome X for males
AnsweredHi GTAK team: I just found the male has the 1/1 genotype on the chromosome X. This should not happen theoretically. a) GATK version used: 4.1.8b) Exact command used: standard WDL scripts provided...
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Shirely commented,
Hi Pamela, Thanks a lot. It works for me.
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Shirely created a post,
GenomicsDBImport: variants have the same position in Gvcf file
AnsweredHi GATK team, I received an error when I running importGVCF task of joint.genotyping.wdl script. This error info is : 18:27:40.775 INFO GenomicsDBImport - Importing batch 1 with 50 samples18:29:28....
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Shirely commented,
Hi Beri, Thanks for your help. Another question: When I do the variant recalibration, should I only use the variants within the intervals or variants within the intervals and outside the interval ...
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Shirely created a post,
What interval should be used when doing the BaseRecalibrator for exome data
a) GATK version used: 4.1.8.0 with dockerb) Exact command used: Exome Germline Single Sample Pipeline in the WARP website Quetion: When I run the BaseRecalibrator for my exome sequencing data, th...
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Shirely created a post,
DetermineGermlineContigPloidy error
a) GATK version used: 4.1.8.0 with dockerb) Exact command used: from the github gatk/scripts/cnv_wdl/germline/cnv_germline_case_scattered_workflow.wdl c) Entire error log: Picked up _JAVA_OPTIONS...
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Shirely commented,
Hi Genevieve I have read and tried all useful posts and suggestions that your team shared, but also got the same error information. Below is the solutions I have tried: 1) Put the sample.g.vcf.gz a...
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Shirely commented,
Hi Viond Kumar, I also have the same problem with you, with the error information like that: A USER ERROR has occurred: Failed to create reader from file:///biomedja01/disk1/lxu/joint-genotyping/A0...