gevro

Hello, Single-cell capture data has a fair number of false positive calls, but the 'weight' column seems to do a good job at filtering them out. Is it reasonable to...

call with filters cn, ci, sem

2

Hi, I'm trying to run call with --filter cn --filter ci --filter sem. But getting this error: ValueError: 'sem' filter requires column 'sem' However, I ran segmetrics with --ci and...

Hi, The threshold parameter of the segment command does not seem to have any effect on final segmentation or post-call step results, when using the cbs method. Is this expected?...

Hi, I ran the latest version of cnvkit via docker with these settings: cnvkit.py batch -n -f REF.fasta -m hybrid -g ACCESSIBLEREGIONS.bed -t PROBESBED.bed --target-avg-size 50000 --antitarget-avg-size 4000000 --antitarget-min-size 1000000...

Hello, The documentation does not specify recommended values for the access -s (mingap) value. What are suggestions for this? Thanks

Possible bug in GenotypeGVCFs 4.6.0.0, affecting all genotyping applications

6

Hi, It seems that for samples in which a variant was NOT detected in a cohort, that GenotypeGVCFs is putting read depth in the AD and DP FORMAT fields of...

vcfR2tidy: behavior when > 1 record at same chrom/POS

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Hi, When a vcf has > 1 record with the same chrom and POS, it would be impossible to join back the gt and the fix data frames to each...

Hi, Question: Is the cytosine report (.CpG_report.txt.gz) analyzed from deduplicated data? Seems like it from the code, but wanted to confirm definitively. Thanks