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Hi Marcel,
I'm sorry for the additional issue, but I just wanted to ask if it was normal to have a significant number of unphased reads (specifically 99.99% of reads were unphased). I installed wha…
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Hi, there.
I'm user of Isaac aligner and isaac variant caller.
I realigned Hiseq reads by Isaac aligner and then called variant by isaac variant caller with following commands.
isaac-align -r /path t…
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I am trying to use the variant-utils comparetwo function to compare two gvcf files from our GATK pipeline. I have tried several iterations of files including converting to vcf using gvcftools (extrac…
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In doing continued profiling of the HaplotypeCaller GVCF mode I have observed that somewhere in the range of 12% of our overall runtime (after i've made my other optimizations) is spent in `VariantCon…
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We should map reads to MT DNA too.
Is it in the reference?
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I tested the GLnexus Docker image, and tried to combine just two of my WGS gVCF samples to familiarize myselft with the program. I got the error message:
Failed to genotype: Invalid: genotyper: une…
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Currently with GLnexus (as I understand it), it creates one output file that contains the regions that are specified in the regions BED file. It would be nice if there was an option for creating one f…
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Hi,
I'm trying to run duet but the SNP calling isn't working.
Thanks,
Melissa
> [INFO] Check environment variables
[INFO] --include_all_ctgs not enabled, use chr{1..22,X,Y} and {1..22,X,Y} …
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Hi all.
This looks like an issue presented by a forum post
[Haplotypecaller FORMAT:DP is affected by the interval in WGS](https://gatk.broadinstitute.org/hc/en-us/community/posts/27992393649051-H…