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Hi! I'm quite new to bioinformatics and I'm running into an issue using krisp_vcf where I get the following error:
(py311) Janehol@bcsumx01:~/krisp$ krisp_vcf krisp_metadata.csv Race_1.masked.fa --…
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Good evening,
`ngsPool` provides `poolSFS.R`, a script which estimates a one dimensional SFS from the `SAF.GZ` output file. Is it possible for other software to read pairs of "sample allele frequen…
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Hi Juliana, Thank you for sharing your genetic QC pipeline—it has been incredibly helpful. I have a question regarding whole-genome sequencing (WGS) data. Due to its large size, it's often to separate…
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Hello!
Previous version of ont-spectre (v0.2.1-alpha) stated that it can use SNV data to detect loss of heterozygosity (LoH) regions does it still apply to current (v0.2.2) version? If so, are there …
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Hello :)
Thank you for this software, it works fantastic!
I have a question about how I can extract a phased VCF file from the haplotagged bam file that I have created. The original VCF that the r…
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I have an allsites vcf, containing invariant and variant sites, that I have properly filtered (e.g., missing data, depth). Since I used vcftools at a certain stage _[to update, I have tried without us…
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Hi，
The program only generates chunked panel data as RData files but does not proceed to the imputation step. When using a different reference panel with the same code, there are no issues; only the …
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Hi developer,
I used your script to calculated the log2afc of my eqtl data. Fortunately, it worked and go…
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Hi - When I try to index multiple VCF files data/*.gz, it only takes the first VCF file for indexing and not all in the directory. Can it only take one input VCF file at a time?
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Hi,
My SLiM simulations include multiple chromosomes (recombination rates are set at 0.5 between them, as described [here](https://github.com/tskit-dev/tskit/issues/176#issuecomment-483839707) ) and …