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Hi
I am trying to use svict for prostate cancer cfdna data and I have trouble understanding the format of the vcf
```
#CHROM POS ID REF ALT QUAL FILTER INFO
1 26608813 . C . PASS SVTYPE=DEL…
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Long TODO lists don't get done.
We are trying to keep an issue open if a real effort is happening to resolve it.
The below priority list gives a sense of where bcbio is heading in the next two rele…
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Please describe:
Hi
I'm trying subcommand "construct" using reference sequence
VCF files that I using is COSMIC's coding/non-coding variants from COSMIC v87 data and dbSNP 150
Also I tried using…
tahuh updated
5 years ago
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Talking with Dr.Sun to ensure the research topic, read the paper "DNA methylation analysis explores the molecular basis of plasma cell-free DNA fragmentation. Nature Communications, 14(287), https://d…
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Hi,
Thanks for the methylation analysis pipeline.
I was testing a human WGBS data with msPIPE, and I used UCSC hg38 for reference. When running with run_MethylSeekR.pl, I got the following error…
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Greetings,
Here is the command we tried on the test bam file (actually, we also tried the program on our own bam files, and get the same result).
`msisensor-ct msi -D -M ./models_hg38 -t ./test…
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In light of #87 and recent work on cfDNA internucleosomal methylation, does it make sense to have a feature in modkit that samples a position-dependent methylation calling threshold?
If something l…
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Thank you very much for the great tool!
I recently found this manuscript from your group:
"The DNA methylome of human vascular endothelium and its use in liquid biopsies"
It complements the ref…
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I'm looking for a way to automate the tracking of reagents using pyclarity-lims. Here I say that a step requires cfDNA_Proteinase_K to be tracked:
![reagents_required](https://user-images.githubus…
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After running this command:
/nfs/sw/bwameth/bwameth-0.2.0/bin/bwameth.py --reference methylation_cfDNA/resources/bwameth/hg19.fa trunc_test/trunc_test.R1.fastq trunc_test/trunc_test.R2.fastq --threa…