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Hi,
```
version: v3.0.1
Files and parameters used:
-e 3000000000
-k 31
-o index/processed
-r chm13v2.0.fa
-t 10
-v merged.sorted.multi.vcf
Determine allele se…
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since i'm converting liftover in these pipelines to scatter/gathers in order to facilitate the ability to perform concordance with either grch37 or 38 genotyping arrays. i should do the gather on the …
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Do you know why for the REF N is displayed? Is there also a way to obtain the ALT sequence?
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GALF003
chr1 789502 440 …
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What do we do? Delete the Genotype record and notify the user?
https://sentry.io/opensnp/opensnp/issues/436275621/
```
Errno::ENOENT: No such file or directory @ rb_file_s_lstat - /home/app/snpr/pub…
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I have a dataset that I am trying to convert to gtc but ran in to an error using bcftools and idat2gtc version 1.20. GEO accession is GSM5579064 and an example that works on the same dataset GSM557906…
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Hi,
I have observed that some variants located at the ends of chromosomes seem to be unsuccessful in genotyping from all samples in my dataset. If this phenomenon is normal? Could you please provide…
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Hi there,
We'd like to try using MALVA on our own low-coverage WGS data (~1x). We've noticed that the MALVA release we're using (version 1.3.1; build h3889886_0) is only genotyping sites where a sa…
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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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We usually filter variants against a panel of normal samples. This can be done post variant calling by genotyping detected variants in this panel and call anything at a certain threshold in a minimum …
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Dear all,
When learning how to detect SVs based on the `pggb` constructed graph genome using `vg giraffe`, I found that the results are a bit strange. And this may be due to the absense of the back…