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Old 06-21-2017, 10:58 AM   #1
MGCBrown
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Default Is indexing .bam files before samtools mpileup necessary?

Is indexing your .bam files a necessary step for running the samtools variant calling pipeline (ie samtools mpileup, bcftools view etc)?

I know that indexing your genome/transcriptome is a necessary step but I can;t figure out if my coordinate sorted .bam files need to be indexed as well.

Thank you!
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Old 06-22-2017, 12:56 AM   #2
dpryan
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Yes, you must index the BAM file too.
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Old 06-22-2017, 11:38 AM   #3
MGCBrown
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Thank you, Devon!
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