Chunyang Bao
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Activity overview
Latest activity by Chunyang Bao-
Chunyang Bao commented,
Yes, you are right! Genotype information is required. Thank you!
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Chunyang Bao commented,
Sure! Example variants from "gs://gcp-public-data--broad-references/hg19/v0/1000G_phase1.snps.high_confidence.b37.vcf.gz" 1 51479 rs116400033 T A 11726.81 PASS AC=229;AF=0.3253;AN=704;BaseQRankSu...
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Chunyang Bao commented,
I ran it on a tumor BAM and a 1000g VCF as follows ... gs://gcp-public-data--broad-references/hg19/v0/1000G_phase1.snps.high_confidence.b37.vcf.gz Thanks, Chunyang
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Chunyang Bao commented,
Yes! I checked the RG info in my bam files and show an example as follows. Furthermore, my bam files worked well with other GATK tools, e.g.mutect2 and Haplotypecaller. @RG ID:H55KF.2 SM:XXX LB:Nor...
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Chunyang Bao created a post,
ASEReadCounter ouputs only header
I am using ASEReadCounter to call allelic read counts on 1000 genome reference. But, I found ASEReadCounter generatd only header in output file. Here I enclosed my command and stderr log. Please he...
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Chunyang Bao commented,
Hi, I can not find "--genotyping_mode" option in this version. Can I assume DISCOVERY mode is the default mode. But, I am wondering if "GENOTYPE_GIVEN_ALLELES" is still being supporated in this ve...