Niharika
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Activity overview
Latest activity by Niharika-
Niharika commented,
Hi Tanay, How did you solve this problem? I am facing same problem.
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Niharika created a post,
SplitNCigar reads tool is not running
REQUIRED for all errors and issues: a) GATK version used:GATK v4.4.0.0b) Exact command used: gatk SplitNCigarReads -R SplitNCigar_Reads/human_genome.fna -I Mark_duplicates/PicardOutput/sorted_uniqu...
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Niharika commented,
Hi Ryan Sun will you please tell me how did you add END tag in the VCF? Also I would like to know if you got an end key reported in vcf at the position where error is thrown? I can not see any END ...
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Niharika commented,
I am using GATK SplitNCigarReads version 4.0.5.1 And getting an error (attached) gatk SplitNCigarReads -R SplitNCigar_Reads/human_genome.fna -I Mark_duplicates/PicardOutput/sorted_unique_reads_with...
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Niharika commented,
Hello, Using sorted bam solved my problem
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Niharika commented,
Hi I am using GATK SplitNCigarReads version 4.0.5.1 And getting an error (attached) gatk SplitNCigarReads -R SplitNCigar_Reads/human_genome.fna -I Mark_duplicates/PicardOutput/sorted_unique_reads_w...
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Niharika commented,
Can this tool be used to call variants from multiple samples? By multiple samples I mean multiple individuals.
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Niharika created a post,
GATK BQSR is taking too long to be run (running since last 6 days)
REQUIRED for all errors and issues: a) GATK version used: 4.0.5.1b) Exact command used:gatk BaseRecalibrator -I Alignment/SRR******_aln_pe_withRG.bam -R GATKBQSR/genome.fna --known-sites GATKBQSR/G...