Mingzhou Fu
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Recent activity by Mingzhou Fu Sort by recent activity-
Okay.... I did some research and found combinegVCF & genotypeGVCF can deal with samples with mixed ploidy (https://gatk.broadinstitute.org/hc/en-us/articles/360035889691-Does-GATK-work-on-non-diplo...
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Got it! Thank you for the links! Now I understand this annotation.
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Thank you!
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Hi there, I actually found the Hrun (named HomopolymerRun) in GATK3.8. I tried to run GATK3.8 VariantAnnotator on my VCF file generated by GATK4. Here's the command module load gatk/3.8.0 ref_ge...
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I see. Thank you very much for the explanation :)
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Gotcha! Thank you Genevieve! Last question regarding your previous suggestions - " I think for your case I would recommend running CombineGVCFs for all samples, but separating the runs by chromoso...
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Thank you Genevieve! Regarding the lost records, is there a quick way to figure out which records were lost? Should I compare the sites/position in gVCF vs the sites/position in combined gVCF?
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I got this WARN when using combineGVCF. I guess this was probably due to my WES were captured with different capture kit (and thus target regions) and I used the union of the target regions (as reg...
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Hi Genevieve, Thank you so much for the reply! If I run WGS and WES separately, how can I put them all together for genotypeGVCF? I want the WGS data from 1KG to joint call together with my sample...
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Hi Genevieve, Since the time & memory limiting step for combineGVCF/importgenomicDB for my ~3000 g.vcf is that the ~2000 WGS g.vcf files are too large to open/read in, I'm wondering if I can use se...