Tagged with #trimming
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Created 2015-10-21 08:15:13 | Updated | Tags: picard trimming readadaptortrimmer

Comments (3)

Hi,

Is there a "Best Practices" for how to use ReadAdaptorTrimmer? To me it seems that there is a Catch 22, if one wants to use GATK and Picard.

According to the ReadAdaptorTrimmer documentation: "Read data MUST be in query name ordering as produced, for example with Picard's FastqToBam". Therefore, I would start by doing

java picard.jar FastqToSam FASTQ={r1_file} FASTQ2={r2_file} OUTPUT={bam_file} SM={sample} SORT_ORDER=queryname

to convert my FASTQ files into a sorted uBAM file. However, ReadAdaptorTrimmer requires the BAM file to be indexed, but if I then try

java picard.jar BuildBamIndex INPUT={bam_file}

it fails because BuildBamIndex requires that the BAM file is sorted by coordinate (which does not make sense since the reads are not yet aligned).

Thanks, Michael


Created 2013-11-26 01:16:34 | Updated | Tags: mutect trimming

Comments (0)

Hi,

GATK 2.7 does not require quality trimming anymore as the tools take base qualities into account. Is it OK to use these untrimmed reads with Mutect as well? Should I expect a big difference comparing the Mutect calls of trimmed and untrimmed versions of the raw reads?


Created 2013-07-15 15:02:11 | Updated | Tags: exome trimming

Comments (7)

Hello,

Sorry if this is the wrong forum for this question - I just thought someone might have an idea/opinion...

Should I trim/filter exome sequencing reads prior to mapping with BWA and variant calling using GATK? I am currently filtering out reads in which <80% of bases have quality>=Q30 but I lose >20% of my reads this way. Does GATK take quality into account therefore rendering pre-mapping filtering unecessary?

Thanks in advance, Kath