HT
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Activity overview
Latest activity by HT-
HT commented,
Hi Genevieve, I understood. Thank you for your kind help! Best, HT
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HT commented,
Hi Genevieve, Thank you for your speedy reply! Noted that it was a bug in old versions. I followed the GATK best practice workflow and used HaplotypeCaller to create gVCF files. Then combined indiv...
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HT created a post,
GATK4.0.3.0 - CombineGVCFs - Unexpected base in allele bases
I have combined 400 gVCFs into two files (S2_200_F1.g.vcf.gz and S2_200_F2.g.vcf.gz), each one includes 200 samples. I am trying to but failed to combine these two files. The error info is Unexpect...
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HT commented,
Hi Pamela, OK, I see. The latest workflow is indeed a better choice. Thank you again for your kind help! Best, HT
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HT commented,
Hi Pamela, Understood, I should always use the same version of GATK. Thank you for your suggestions! They are really helpful! Could you please help to submit a Github ticket? I would indeed like to...
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HT commented,
Hi Pamela, Thanks for your quick reply! I reindexing the fast file using samtools as you suggested. Now it works with GenotypeGVCFs in GTAK version 4.2.1.0 using old fasta data. I was wondering whi...
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HT created a post,
GATK4.0.3.0 GenotypeGVCFs - Could not open array genomicsdbarray
a) GATK version used: GATK 4.0.3.0 b) Exact command used: [Tool]: GenomicsDBImport export TILEDB_DISABLE_FILE_LOCKING=1time ${dir_tool_gatk}/gatk --java-options "-Xmx85g -Xms85g" GenomicsDBImpor...