Laura Gauthier
- Total activity 44
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 0
- Subscriptions 19
Activity overview
Latest activity by Laura Gauthier-
Laura Gauthier commented,
Is LowGQX a float or an integer? That could be the main problem. The code that's being called in the expression all comes from htsjdk, mostly the VariantContext class:https://github.com/samtools/h...
-
Laura Gauthier commented,
Hi user105689, The picard code says If this interval is in the opposite orientation, all alleles and genotypes will be reverse complemented and indels will be left-aligned. I don't see any explici...
-
Laura Gauthier commented,
Hi Sheryl, These are whole-genome samples? I don't have great intuition here because I've done much more work on the germline side, but I think it's worth trying both approaches: with the Illumina ...
-
Laura Gauthier commented,
Hi Yuwei Bao, The sites file can be specific to your data (e.g. from HaplotypeCaller results) or based on common variation like the 1000 Genomes SNP file from the VQSR resource bundle: https://gatk...
-
Laura Gauthier commented,
Hi Marissa Eronika, This is expected behavior for the tool -- the FORMAT field also has a FILTER attribute. If you want to generate an INFO-level filter based on genotype-level data the easiest wa...
-
Laura Gauthier commented,
Hi Shashank Shekhar Padhi, This has been an issue since the beginning of time and I can suggest a variety of workarounds. If you're really intent on having a single VCF file, then you'll need to f...
-
Laura Gauthier commented,
Hi Nils Paffen, Do you mean phasing by haplotype or phasing by transmission? If you have related samples, then supplying a pedigree file to the CalculateGenotypePosteriors tool will apply Bayesian...
-
Laura Gauthier commented,
Great news! I will make the changes in the gCNV article so this doesn't happen to anyone else.
-
Laura Gauthier commented,
The recommended file for hg38 exomes is gs://gatk-sv-resources-public/gcnv-exome/contig_ploidy_prior_hg38.tsv. The ploidy_prior columns refer to the copy number of the contig of interest and the v...
-
Laura Gauthier commented,
Hi Sophia I'm not a bash ninja, but I think there's a format conversion bug in the code on the forum. I suspect ">" is supposed to be ">" so that the output of awk is directed to an output file ...