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Old 06-02-2012, 06:54 AM   #1
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Default target region file for samtools (.bed file)


I just started to use samtools to call SNPs on some target regions for crop wheat, should I sort the .bed file by chromosomes and start and end Or samtools accept unsorted .bed file so that chr has to be in order, as well as start and end positions from small to large?

eg, my bed file looks like:
chr1 2345 34565
chr1 3455 65421
chr1 23455 23299

thank you,
lifetech01 is offline   Reply With Quote
Old 07-09-2014, 03:59 PM   #2
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you can first sort and index your bam file. then why not use bed tools to create a bed file from your sorted bam file?
arcolombo698 is offline   Reply With Quote

bedfile, samtools

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