Sinem Selvi
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Activity overview
Latest activity by Sinem Selvi-
Sinem Selvi commented,
Thank you! NuMTFilterTool looks better to use.
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Sinem Selvi commented,
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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Sinem Selvi created a post,
--interval-padding range differs called variants
REQUIRED for all errors and issues: a) GATK version used: gatk-4.3.0.0b) Exact command used:$GATK --java-options "-Xmx"$memory"G -XX:ParallelGCThreads=$thread" HaplotypeCaller -R $GENOME_FASTA -I $...
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Sinem Selvi commented,
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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Sinem Selvi commented,
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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Sinem Selvi created a post,
disabled all read filters but reads are still filtering
Hello,I'm working on UMI included data and had UMI aware deduplication step. But still, the haplotypecaller removes most of the reads even though the log file shows "0 read(s) filtered by: NotDupli...
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Sinem Selvi commented,
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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Sinem Selvi created a post,
depth of indel in a uncalled snp site
Hello, There is an indel called by HaplotypeCaller with a high allel depth(61), but in IGV the count of indel is 12 . The location has C alell but it is uncalled. I checked near sites and there is ...
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Sinem Selvi commented,
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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Sinem Selvi commented,
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...