yfarjoun
commented
4 years ago You could filter with a javascript that will look at the mapping quality, and filter accordingly, instead of extracting the list of reads that have high enough mapping quality and then filtering by read name.....
alternatively, you could also set SORT_ORDER=queryname, or SORT_ORDER=coordinate and rerun your commandline.
Y.
On Tue, Nov 19, 2019 at 6:06 PM Alva Rani James notifications@github.com wrote:
Dear All,
I am using Picard FilterSamReads for filtering a list of sorted reads from a read_name/_id sorted BAM file. I am wanna sort the list of reads which are of certain mapping quality.
Here is what I tried,
java -jar -Xmx4G /path/picard-2.18.4-0/picard.jar FilterSamReads I=simulate_50X_pat_sorted_read.bam O=simulate_50X_pat_sorted_quality_pat.bam READ_LIST_FILE=pat_quality2 FILTER=includeReadList
And the above line is throwing the following error,
INFO 2019-11-19 16:51:40 FilterSamReads Filtering [presorted=true] simulate_50X_pat_sorted_read.bam -> OUTPUT=simulate_50X_pat_sorted_quality_pat.bam [sortorder=queryname] ERROR 2019-11-19 16:51:40 FilterSamReads Failed to filter simulate_50X_pat_sorted_read.bam java.lang.IllegalArgumentException: Alignments added out of order in SAMFileWriterImpl.addAlignment for file:///cluster/work/projects/simulate_50X_pat_sorted_quality_pat.bam. Sort order is queryname. Offending records are at [1-93166-:1-93466--:::::::::::52438MzI4MTAy:1] and [1-102419--:1-102119-:::::::::::199592NzM1MA==:1] at htsjdk.samtools.SAMFileWriterImpl.assertPresorted(SAMFileWriterImpl.java:213) at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:200) at picard.sam.FilterSamReads.filterReads(FilterSamReads.java:256) at picard.sam.FilterSamReads.doWork(FilterSamReads.java:345) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113) [Tue Nov 19 16:51:40 CET 2019] picard.sam.FilterSamReads done. Elapsed time: 0.20 minutes. Runtime.totalMemory()=3706716160
I have tried to remove the above reads from my input list and tried again, however, the same ERROR message appeared with different read names.
I would like to know, what else other than sorting the inputs should be done before running the FilterSamReads tool?
Any help or suggestion is much appreciated.
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moldach
Dear All,
I am using Picard
FilterSamReadsfor filtering a list of sorted reads from a read_name/_id sorted BAM file. I am wanna sort the list of reads which are of certain mapping quality.Here is what I tried,
And the above line is throwing the following error,
I have tried to remove the above reads from my input list and tried again, however, the same ERROR message appeared with different read names.
I would like to know, what else other than sorting the inputs should be done before running the
FilterSamReadstool?Any help or suggestion is much appreciated.