zhenxian

Hi, We confirmed it was a bug from WhatsHap. Sadly, we could not do more before WhatsHap fixed it. We suggest you use `LongPhase`, which performed comparably to WhatsHap with...

Hi, @haraldgrove, Could you please provide us with the pileup result of the flanking 10bp windows? This will help us pinpoint the genotype issue more accurately. To obtain the mpileup...

Hi, @haraldgrove, Thanks for providing the BAM, it seems the Clair3 pileup model made an incorrect zygosity prediction due to the insertion variant was followed by a deletion immediately. Could...

Hi, @sloth-eat-pudding, Thank you for your interest in ClairS. 1. Our design is to select heterozygous SNPs from both normal and tumor samples for phasing and haplotagging. These signals are...

For Q1, seems there are no homozygous variants in normal BAM in Figure 2, are you referring to a homozygous reference(that is the same allele as the reference base)? But...

@sloth-eat-pudding Glad to have the new release of LongPhase, our team will test it and get back to you. ZX

@RenzoTale88 Thanks for raising this. The space in the input path leads to parser error. We have tried to add path quotation but find it hard to cover all the...

@nparmalee Could you share `logs` directory and `run_clairs.log` log file in your output dir `/home/nparma/eee_bams_dsa/myanalysis/clairs/T/dsa/clairsout` for us to pinpoint the issue? My email address is [email protected], thanks.