Tagged with #softclip
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Created 2014-06-02 22:01:51 | Updated | Tags: clipreads bug softclip fixmisencodedquals
Comments (1)

I was softclipping some 84-bp-long single end reads using the following command:

java -Xmx2g -jar /GATK_Path/GenomeAnalysisTK.jar -T ClipReads -I imput_file.bam -o output_file.bam -R $ALIGNREF --cyclesToTrim "1-4,80-84" --clipRepresentation SOFTCLIP_BASES --fix_misencoded_quality_scores

There was no error while running, but when I looked at the file afterwards, every read had a cigar string of 84S. I'm fairly sure this is a bug. I was aligned to the human mitochondrial genome.

I am using GATK v2.3-9-ge5ebf34 on Mac OS 10.75


Created 2012-12-20 01:21:50 | Updated | Tags: indelrealigner softclip
Comments (1)

Hi, Some aligners produce Smith-Waterman alignments and may soft clip bases from a read when there are indels or mismatches near the ends of the reads. I was wondering if you include these bases in the realignment process? And if not whether you might consider making it an option? Thanks, Colin