rq m
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Latest activity by rq m-
rq m commented,
I set the parameters as follows: gatk GenotypeGVCFs \ --reference $ref_path \ --include-non-variant-sites \ --variant gendb://$variant_dir \ --genomicsdb-max-alternate-alleles 151 \ ...
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rq m created a post,
Has too many alleles in the combined VCF record
I used GATK 4.3.0.0 to call SNPs and INDELs according to the following process:HaplotypeCaller + GenomicsDBImport + GenotypeGVCFs gatk GenotypeGVCFs \ --reference $ref_path \ --include-non-va...
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rq m created a post,
How can I get Sample Summary
I want to get the number of SNP, Indel and MNP in each sample. In the overview of VariantEval, it said "These metrics include number of s per sample". And "Sample and variable summary" is mentioned...
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rq m commented,
Hi Genevieve Brandt. Thanks for your answer.I have understood question 1 and 2, but I still have doubts about question 3.I have used version 4.2. I called CNV according the tutorial (How to) Call c...
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rq m created a post,
Three questions about calling CNV in Germline.
AnsweredQuestion 1:I noticed that there is a sentence in the description of GermlineCNVCaller: providing a cohort of germline samples sequenced using the same sequencing platform and library preparation p...
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rq m created a post,
what's the meaning of "WARNING gcnvkernel.structs.metadata - Sample XXX has an unrecognized contig(contig_name). Germline contig ploidy determination may not be reliable for decoy/non-standard contigs." in CNV Calling?
I use Docker GATK 4.2.0.0.I want to detect CNV in Saccharomyces cerevisiaeI use the following command gatk DetermineGermlineContigPloidy-L cohort.gc.filtered.interval_list \--interval-merging-rule...