Tag: MergeSamFiles

Efficiently merge two BAM files while retaining reads from only one file in overlapping regions

Efficiently merge two BAM files while retaining reads from only one file in overlapping regions 1 I have a WGS BAM file that is fairly large (>150GB) and a smaller BAM file (<5GB) with reads in a small 10Mbp region. I want to (efficiently) merge the two BAM files while…

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Can I sort my bam files with Picard MergeSamFiles?

Can I sort my bam files with Picard MergeSamFiles? 0 Hi! I noticed this in the picard MergeSamFiles help: –SORT_ORDER,-SO:SortOrder Sort order of output file Default value: coordinate. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Does this mean that it is unnecessary to use picard SortSam before? can MergeSamFiles do…

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