can you elaborate more on this?
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unsorting a bam file
I have some data with high PCR duplicates that I need to deduplicate with Picard MarkDuplicates. However, the outputted bam from Picard needs to be unsorted for the downstream program using the output of Picard.
I tried running picard with ASSUME_SORT_ORDER unsorted, but got the following error:
9 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
10 picard.PicardException: This program requires input that are either coordinate or query sorted (according to the header, or at least ASSUME_SORT_ORDER and the content.) Found ASSUME_SORT_ORDER=unsorted and header sortorder=unsorted
Either (1) is there a way to unsort a bam file from Picard? (2) is there a way to run Picard on an unsorted bam file, which the documentation suggests but this error message implies otherwise?
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wiscoyogi •
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as best Picard Tools can tell your BAM file is unsorted, but to mark duplicates your input needs to be a BAM file that is sorted by genomic coordinates, see documentation for details: https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates
For sorting a BAM file see samtools sort http://www.htslib.org/doc/samtools-sort.html
my problem is that the program im feeding the de-duplicated files to requires an unsorted bam file.
is there a way to unsort a bam file?
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