User: Yatros

gravatar for Yatros
Yatros10
Reputation:
10
Status:
New User
Location:
USA / Seattle / University of Washington
Last seen:
1 year, 2 months ago
Joined:
1 year, 3 months ago
Email:
o**************@gmail.com

Posts by Yatros

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Problem parsing interval list file to GenomicsDBImport in GATK4
... Hello, I know that this solution is not elegant, nor solves the issue of adding the GenomicsDBImport command to a WDL pipeline, but for now, this is what works best for me: #!/bin/bash java -jar $GATK GenomicsDBImport -V sample_001.gvcf.gz -V sample_002.gvcf.gz -V sample_003.gvcf.gz -V sam ...
written 15 months ago by Yatros10
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Comment: C: Problem parsing interval list file to GenomicsDBImport in GATK4
... By the way, I already switched to GATK4.beta.6 and the problem with this script persists, Thanks, ...
written 15 months ago by Yatros10
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Comment: C: Problem parsing interval list file to GenomicsDBImport in GATK4
... Dear Pierre-Lindenbaum. I already checked this. My reference file has no 'chr' notation. This is how the first line of my .dict file looks like: @SQ SN:1 LN:249250621 Thanks anyway ...
written 15 months ago by Yatros10
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Comment: C: Problem parsing interval list file to GenomicsDBImport in GATK4
... The output from this grep is the following one: 1#8022745#8023035 I do not think that GenomicsDBImport is recognizing the input file in the right way. And I think that the input file should have the following format 1:8022745-8023035. When I do a script using with WDL+CROMWELL with the input file ...
written 15 months ago by Yatros10
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Comment: A: Problem parsing interval list file to GenomicsDBImport in GATK4
... Hello, I have tried to handle this issue with a WDL + CROMWELL script, but I am still facing a problem. I will detail my input files and my script to see if you can help me solve the problem. I am running the following command: java -Dconfig.file=application.conf -jar $CROMWELL run my.wdl --i ...
written 15 months ago by Yatros10 • updated 15 months ago by RamRS20k
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Problem parsing interval list file to GenomicsDBImport in GATK4
... Hello, I'm trying to combine 6 GVCF files into a single VCF file using GATK4 GenomicsDBImport + GenotypeGVCFs. I'm still using GATK4.beta5, since I'm not able to find the link to GATK4.beta6. My target.interval file looks like this: 1:8022745-8023035 1:8025283-8025585 1:8029304-802956 ...
gatk parsing interval gvcf written 15 months ago by Yatros10 • updated 11 months ago by prnsml0

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