Tagged with #softclip
0 documentation articles | 0 announcements | 3 forum discussions

No posts found with the requested search criteria.
No posts found with the requested search criteria.

Created 2015-08-11 14:01:44 | Updated | Tags: haplotypecaller softclip soft-clipping
Comments (27)

Dear GATK team, From what I read on the forum, it seems that HaplotypeCaller call variants (and perhaps calculates RGQ) using soft-clipped parts of the reads? Is there a parameter to suppress this behavior, making it throw out the soft-clipped proportions before calling? Best regards, Ray

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