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Hi,
I am having an issue with the extraction of the RD and AD genotype tags in my input VCF file to the 'gt_ref_depths' and 'gt_alt_depths' columns of my gemini database. I am using gemini (v0.8.0) o…
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I run the ~last~ latest version of vcf2maf on my data. I want to obtain ~vcf~ VAF comparable to data from TCGA.
I could not find VAF in the maf file of variants from tumor and normal
`"vcf2maf.pl --…
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Hello,
I am trying to run SomaticSeq on RNA data (single-end reads) but it's really slow. It never finished because I had to kill it after 7 days. I have many large samples (~10 GB) and if the smal…
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Hello. Thank you for developing this great tool!
I tried to use "vcfFilter_DP_Freq.pl" commend on my system, yet I cannot find which format I need to adhere for each parameters.
From the guidelin…
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Hello,
I have HiSeq data from some yeast experimental populations and I would like to compare population parameters between populations (samples). For example, I would like to estimate genetic divers…
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After preparing the required input, the pipeline can't seem to find the specified files or output directory. I don't see in the log files whether or not my sample file is recognized. I am hoping that…
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Our pipeline already spends quite some time producing pileups for VarScan and we also wanted to enable FREEC BAF. I decided to use the pre-existing pileups with `inputFormat=pileup` and `SNPfile` inst…
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It looks like the repository is only being used to keep snapshots as JAR files. Is there anywhere I can checkout the source to see version history? For example, I want to see when default parameters c…
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Hi,
Thanks for a great program!
I'm getting an error 'Something is not right with your vcf file' and I'm wondering if there are VCF file specifications that need to be met to use this tool? I'm not…
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Hey,
Thanks for developing the SCmut tool. I am trying to use it on my own data, but my tumor- and normal- bulk bam file are all generated based on hg38. I try to use `gatk mutect2` to call somati…