Mobin Asri

Hi Martin! Thanks for asking. Yes I'm definitely interested in finishing what we have started. I have been busy doing some other projects but I can plan to dedicate some...

Hi, They are in the coordinates of chm13v1.1.

Hi @andosl Thanks for using Flagger. It should be robust to median or mean as long they are not highly different but median is better. Since Flagger only uses the...

Hi @MariBGO Sorry for the late response. As long as you have an assembled sequence and you know the expected coverage along your desired regions you should be able to...

Hi @kiratalreja3 Thanks for using Flagger. The best way to use Flagger is by running the WDLs prepared for this aim. Please read [this part](https://github.com/mobinasri/flagger#running-pipeline-with-wdl).

Hi @ericgonzalezs Yes you can use "flagger_end_to_end_no_variant_calling_no_ref.wdl" using the instructions mentioned here: https://github.com/mobinasri/flagger#running-pipeline-with-wdl It ignores incorporation coverage biases in HSats.

Hi @Enorya If you could share your cov.gz file I would be able to reproduce your error on my side and help you better.

@DustinSokolowski By phased read mappings I meant having each read mapped to the correct haplotype assuming that the assembly is phased and diploid. There is no need for haplotagging bam...

HMM-Flagger assumes that each haplotype is assembled in a separate contig. It does not care about phasing switch errors. As long as both copies are assembled it works fine. However...

@baozg Thanks for reporting this. It is not obvious to me what is worng. Can you test flagger-v1.1? If you could provide the cov.gz file and those bed files I...