Homa

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Homa
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Homa Papoli

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  • @Sheila Hi, BP_RESOLUTION does not give MQ for non-variant sites. What I think I will use now is getting the callable/uncallable sites annotations with "Low mapping quality" so I can at least filter sites for mapping qualities in a more …
  • I would also like to have a document on the type of change that has been applied to use HC for RNA-seq data.
  • @tommycarstensen‌ , this is a pool of 2 individuals, so, the ploidy should be set to 4.
  • Thank you for your answer. Are the large number of scaffolds the problem only for Haplotype caller or for the whole utilities of GATK? For example for Indel Realigner as I have already run this tool. Thanks for your help.
  • @‌Sheila Hi, Thank you very much for your answer. I am sorry but I don't completely understand what I should do: "In that case, we recommend combining subsets of scaffolds into artificial contigs (with appropriate spacers) to reduce performa…
  • I also have another question regarding the use of the reference genome. My reference genome assembly has only the information of scaffolds, so, we don't know which scaffold belong to what chromosome. I read in a documentatin that for GATK, the refer…
  • Thank you very much for your reply. I will let you know about my experience.
  • Sure, I will soon provide you with some examples, thank you for your replies.
  • Regarding alignment, I have a question too, as follows: I have individual-based RNA-seq data for 6 female birds. So, previously, a researcher in the lab, had used pooled data of 3 individuals. She had used the pooled data to do the SNP calling. The…
  • Hi vyellapa, I am aligning my RNA-seq reads against a de novo transcriptome assembly, for that, I have used BWA. However, I have received some advice from a bioinformatician that to align the RNA-seq against a genomic reference, you better not to u…
  • For the bam file, what do you mean by the 'new bam generate in each iteration'? because I have one original bam file and then I use that for snp calling which gives me the vcf files but the bam file itself doesn't change. thanks in advance for your …
  • Yes, I created the .bam files myself, thank you for your explanation, it is more clear to me now what I should do, I will track the problem.