MatZ
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Latest activity by MatZ-
MatZ commented,
No, we downloaded and installed GATK locally. For pre-processing/alignment step we used this: https://github.com/gatk-workflows/gatk4-data-processing/archive/master.zip Into the file folder there i...
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MatZ commented,
That's the point. In the documents there is no mention of an alt file but in the file processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json there is. There are references about all index file...
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MatZ created a post,
bwa index doesn't create .alt file in hg38
AnsweredWe are using Gatk 4.1.4.1 to call somatic variant in the only tumor mode in hg38. We performed sequencing through an amplicon-based targeted gene panel. Due to the presence of another copy of a gen...
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MatZ created a post,
How to keep MAPQ on multiple mapping reads
We are using Gatk 4.1.4.1 to call somatic variant in the only tumor mode in hg38. We performed sequencing through an amplicon-based targeted gene panel. We are not able to call variants validated...