chenglei
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Activity overview
Latest activity by chenglei-
chenglei created a post,
what is a Good Cigar?
Answeredgatk BaseRecalibrator module has a parameter named "GoodCigarReadFilter", Can anyone explain what is a good cigar string more specifically？ 150M is a good cigar, then what about 10S100M40H? I did ...
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chenglei commented,
Can you explain what is a good cigar string more specifically？ 150M is a good cigar, then what about 10S100M40H? I did not find a good explaination in SAM specifications. Hope your response
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chenglei created a post,
germline mutation calling using per-sample module
AnsweredHi,I'm a newer to gatk. I try to use gatk to call germline mutation from my tumor data. I see that there are to modules, per-sample and joint genotyping, I wonder that per sample module compatible ...
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chenglei commented,
Hi,I'm a newer to gatk. I try to use gatk to call germline mutation from my tumor data. I see that there are to modules, per-sample and joint genotyping, I wonder that per sample module compatible ...
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chenglei created a post,
af-only-gnomad.vcf.gz for hg19
Answeredwhere could I find af-only-gnomad.vcf.gz for hg19, I just found af-only-gnomad.vcf.gz for hg38, I check https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg19/v0;ta...
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chenglei created a post,
Values for InbreedingCoeff annotation not detected for ANY training variant
AnsweredWhen I use gatk VariantRecalibrator module to call germline mutation, a error occurred: A USER ERROR has occurred: Bad input: Values for InbreedingCoeff annotation not detected for ANY training var...
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chenglei created a post,
MerVcfs did not work
when I used gatk MergeVcfs module to merge multiple vcf files, several errors were gave as following: gatk MergeVcfs -I SCA_957_N.germline_raw.vcf -I SCA_917_N.germline_raw.vcf -O merge.vcf Using G...
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chenglei commented,
is a dbsnp file in HaplotypeCaller and a couple of other programs (e.g. GenotypeGVCFs) a file like dbsnp_146.hg38.vcf.gz, if germline mutation calling for Homo_sapiens?
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chenglei created a post,
How to get sample coverage files in WIG (wiggle) format using gatk Mutect
When I use MutSigCV to call significantly mutated genes, a coverage file was required. As pointed by the document of MutSigCV, this coverage file can be deriveed from processing sample coverage fil...
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chenglei commented,
my tumor sample are from different individuals