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Hi,
We have 10x data from a cell village and I am trying to identify donors in the village using donor assignment. I have the 10x bam file, barcodes.tsv, gtf and vcf files.
Step 1: I ran Drop-seq…
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Change gene.iobio to show variants and depth (from alignments) for genes on alternate contigs.
For example, gene GSTT1 for build GRCh38 (RefSeq transcripts), the app is not able to display variants…
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Currently the command line documentation for `-p` explicitly excludes VCF files with `For VCF please see option --vcfFile`.
I see no reason for this restriction. `-p` should support reading of `.vc…
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## Describe the issue
I'm annotating a vcf coming from Manta. In the output, some of the variants are not annotated and I don't know why. In my vcf, all the variants have all fields information (incl…
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In our initial use case, we have the comfort of a deterministic mapping between chromosomes and actual VCF files, i.e. `chr4` always exists only on a specific file named in a GREGoR data table.
I'm…
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Hi,
I'm trying to used fine-mapped results of complex traits from SuSiE as the input of fastENLOC as you recommended. I notice the following code you provided in input.md to help contrust the input…
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### Description
Hi,
I am working with tumor only vcf files generated by Balsamic from different versions. To be precise I am using `SNV.somatic.xxx.vardict.clinical.filtered.pass.vcf` files. It co…
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Hi,
I am currently benchmarking tools that balance "compression and accessibility" for genotype data and encountered an issue when using XSI with large datasets. I hope you can assist me in resolvi…
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I received the following error when running PAINTORpipe in with AFR as population
`Traceback (most recent call last):
File "/usr/local/bin/CalcLD_1KG_VCF.py", line 268, in
if __name__ == "…
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I've been trying to use this program to run an MK test using VCF files from the 1000 genomes project. However, I'm getting some really strange results with this method, and I'm worried I may be doing …