Sinem Selvi
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Recent activity by Sinem Selvi Sort by recent activity-
--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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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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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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issue while running mitochondrial analysis
AnsweredREQUIRED for all errors and issues: a) GATK version used: 4.1.9.0b) Exact command used: $GATK --java-options "-Xmx"$memory"G -XX:ParallelGCThreads=$thread" PrintReads -I $SAMPLE_DIR/BQSR_output/rec...
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depth of coverage total summary should not be 100.0
AnsweredREQUIRED for all errors and issues: a) GATK version used: v4.1.9.0b) Exact command used: $GATK --java-options "-Xmx"$memory"G -XX:ParallelGCThreads=$thread" DepthOfCoverage -R $GENOME_FASTA -O $B...