Fiona Liang
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Activity overview
Latest activity by Fiona Liang-
Fiona Liang commented,
Some answers are explained like this: GATK assigns the genotype "0/1" for single nucleotide variants (SNVs) instead of "1/1". Is it true?
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Fiona Liang created a post,
GT values of VCF file generate by Mutect2
Hi All, I ran the "Somatic short variant discovery" pipeline on my WES data and I found only 2 kinds of values in GT(0/1 and ./.). I wonder whether all my SNVs are heterozygous sites. Thank you in ...
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Fiona Liang commented,
Hi, Thank you. I'm still confused because the terra bucket on google clould is different form AlignAndCall.wdl. Steps in AlignAndCall.wdl are equal to those described in gatk mitochondrial best pra...
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Fiona Liang commented,
Hi developer, Thank you for your reply. Where can I find files(or functions) called by AlignAndCall.wdl ? Program files in google cloud of terra are a little bit different from AlignAndCall.wdl. > ...
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Fiona Liang commented,
Thank you so much!
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Fiona Liang created a post,
gtf file for hg38_v0_chrM_Homo_sapiens_assembly38.chrM.fasta
Hi all, I use hg38_v0_chrM_Homo_sapiens_assembly38.chrM.fasta which download from > https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg38/v0/chrM;tab=objects?pref...
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Fiona Liang created a post,
What's the right order of Mitochondrial pipeline
Hi all, I run mitochondrial best practice pipeline as following > https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels- The filtering st...
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Fiona Liang created a post,
Mitochondrial LiftoverVcf
I run Mito pipeline follow : https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels- However, the LiftoverVcf step is really confusing. In...