Yiguan Wang
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Activity overview
Latest activity by Yiguan Wang-
Yiguan Wang commented,
Hi Genevieve, Whether I use " -A StrandBiasBySample" or not seems no difference on my data. gatk GenotypeGVCFs -R dmel-all-chromosome-r5.44.fasta \-V gatk_parent_offspring.g.vcf.gz \-L 2R:207682...
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Yiguan Wang commented,
Hi Genevieve, thanks a lot for your reply. I've read the post you mentioned, but I don't think it answers my confusion. I did some post-HaplotypeCaller filtering, but I am afraid it may not remove ...
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Yiguan Wang commented,
Hi Genevieve, I can confirm the SB annotation exists in the g.vcf file. But it disappears in the vcf file after using "GenotypeGVCFs". Here is the example of vcf file: https://drive.google.com/fil...
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Yiguan Wang created a post,
Artificial haplotype generates a new variant for a homozygous site
Hi, I am using the following command to call variants: gatk HaplotypeCaller \ -R dmel-all-chromosome-r5.44.fasta \ -I ../121002_I637_FCD1B4GACXX_L1_SZAXPI015086-62.sort.noDup.realign.bam \ ...
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Yiguan Wang commented,
Hi Pichu, I encounter the same problem as you described. I failed to obtain the "SB" annotation in the VCF file. I am wondering have you solved your problem, and could you share your solutions? Tha...
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Yiguan Wang commented,
Currently working on Drosophila genomes, there isn't a known list of variants. Just wondering how to perform bootstrap to generate a set of known variants, is there a pipeline about that? Thanks in...