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I ran snphylo and got the error below: did not have DP information and only recognizing chromosome. Please any suggestion?
snphylo.sh -p 25 -v pcap-test1.vcf
Start to remove low quality data.
Warnin…
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Hi, I am running a multivariate analysis, but I discovered MTAG is dropping a whole lot of SNPs due to inconsistent allele. Is there a flag to include to retain this inconsistent allele, or a method …
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following the instructions and having downloaded the sample data as instructed here: https://github.com/hakyimlab/MetaXcan/tree/v0.6.11
using these commands as per the example:
./MetaXcan.py \
--…
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Dear developers,
I encountered an issue with RGsets that contain both EPIC and IL450k arrays - created with combineArray(). It seems that getSnpBeta() doesn't work properly on the combined RGset.
…
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Hi there,
I'm looking for a good method to combine calls produced by short variant callers (50bp). Most structural variant merging tools are designed to merge SVs from different SV callers, and SNP…
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Are there any obvious reasons for this? I used GATK add read groups, mark duplicates, and SplitNCigar reads beforehand. I am just using snp-counts to count reads for a different purpose with an RNA-se…
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Hi, thanks for developing this tool for genotyping. I performed SNP calling with cellsnp-lite, with either (7.4M SNPs with minor allele frequency (MAF) > 0.05) or (36.6M SNPs with minor allele frequen…
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Hello
I am using vcftools to convert vcf file to the 012 format:
`vcftools --vcf sar.vcf --012 --out sar2`
I am getting the following line in the log file:
> After filtering, kept 19402 out of …
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Hi,
I am combing results from hapsb_ind() output using the pp_individual_roh() and I don't want to add meta information. But pp_individual_roh() throws me an error even if I do meta_info=False. I…
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Hello,
I was trying to hard-filter the vcf files outputed by GATK HaplotypeCaller, and I want to keep variants that meet the following condition: depth (QD) < 2.0 || FisherStrand (FS) > 60.0 || root …