I am using Homer and going to build data visulization graph using bedtools, I have two input files one is outputPrefix.bam and second is outputPrefix.bam.bai
when I run bedtools genomecov -i (means bam input file but sorted, but sorted file .bam.bai extension) and secondally when i run this command bedtools genomecov outputPrefix.bam.bai -g hg19 it says that yourfile first line is less then 3 columnis this tabdeliminated?
and when i run bedtools genomecov outputPrefix.bam -g hg19 it runs some process in bash
can any body explain me this problem
1 answer
Bedtools documentation: http://bedtools.readthedocs.org/en/latest/content/tools/genomecov.html
If using BED/GFF/VCF, the input (-i)
If the input is in BAM (-ibam)
When you run -i with your bam bedtools expects bed file as input.
Pgibas has a true, better for you will be validation of your bam file : http://broadinstitute.github.io/picard/command-line-overview.html#ValidateSamFile
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My question is I have bam file which is not sorted one is bam.bai which is sorted but bedtools -Ibam takes file with .bam sufffix so how to input sorted file in genomecov -ibam filename.bam -g hg19
Delete this as this is not answer.