Sinem Selvi
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Recent activity by Sinem Selvi Sort by recent activity-
Hello, What is the recommended method to combine indel and snp VCF files after applying hard filters separately? Thank you!
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Thank you! NuMTFilterTool looks better to use.
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Hello,According to the MT pipeline, this step is calculated after subsetting to chrM. Only chrM is present in the BAM file. How can the autosomal coverage be calculated? There seems to be an issue ...
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Thank you SkyWarrior The problem is solved after submitting the target regions. Do you know why the target file affected depth for the variants for that much?
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Hi SkyWarrior Thank you so much. I think that was one of the reasons. The depth increases to 694 but still less than the input bam file. I will keep this parameter for this data. Do you have any ot...
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1- represented bam file is output of HaplotypeCaller. 2-Actually before solving the problem, I would like to know what caused the issue of not matching variant informations on hc bam and vcf file? ...
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Hello James Emery It might be rounding as it is small number of bases. But when we work on single genes, total coverage is considered in detail. I created the gene list from refseq as explained in ...
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Hello James Emery thank you for your answer. You can see sample_gene_summary result below. Gene total_coverage average_coverage S19_total_cvg S19_mean_cvg S19_granular_Q1 S19_gran...
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Hello,Thank you to consider the issue. The coverage covers the exon. You can find the interval list below. The gap occurred in the first exon of the interval list (chr15:48936802-48936966). chr15...
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Thank you!