Yokofakun
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Recent activity by Yokofakun Sort by recent activity-
CombineGVCF with a mix of gatk3 and gatk4 gvcf files.
Hi all, I've been given a set of precomputed gvcfs files. Some of those files were computed with gatk3.8 , while some other were computed with gatk4.* Do you any any consequence (genotype, scor...
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GermlineCNVCaller/denoising_config.json
AnsweredHello GATK Team, I'm trying to run **GermlineCNVCaller** in CASE mode but I got the exception below. `File not found denoising_config.json` I must say, I'm not sure I understand the workflow in "ca...
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Haplotype Caller (4.1.6.0) : java.lang.IllegalStateException: Smith-Waterman alignment failure.
Can you please provide a) GATK version used b) Exact GATK commands used c) The entire error log if applicable. following https://gatk.broadinstitute.org/hc/en-us/community/posts/360059684672-Cust...
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Custom ReadFilter to ignore malformed reads ?
Hi GATK team, it's not a problem with gatk (currently 4.1.5.0) but with a bam processed with bwa but containing a few reads with a cigar string starting with a Deletion. <pre> org.broadinstitute...
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CombineGVCFs 4.1.2.0 throws "java.lang.IllegalArgumentException: Features added out of order:"
AnsweredHello GATK team, I'm trying to combine GVCF with 4.1.2.0 that were generated with 4.1.1.0. But I got an error. I saw some reference about this error in an old post saying it should have been ...