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Tag: MergeSamFiles
linux merge multiple files in picard
Why not use samtools? for folder in my_bam_folders/*; do samtools merge $folder.bam $folder/*.bam done In general, samtools merge can merge all the bam files in a given directory like this: samtools merge merged.bam *.bam EDIT: If samtools isn’t an option and you have to use Picard, what about something like…
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…
Strange speed up in GATK LeftAlignIndels
Strange speed up in GATK LeftAlignIndels 1 Hi! I noticed a strange thing, I have been running a DNA-seq pipeline like this: reads -> bwa-mem2 -> picard SortSam -> picard MergeSamFiles -> picard MarkDuplicates -> gatk LeftAlignIndels … gatk LeftAlignIndels has always taken around 4 hours to complete with the…
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…