BEDTools genomecov command and input file isse

Question

[Azhar]

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

[Azhar]

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

Answer 1

[PoGibas]

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.

[Korsocius]

Pgibas has a true, better for you will be validation of your bam file : http://broadinstitute.github.io/picard/command-line-overview.html#ValidateSamFile

[Azhar]

Kindly could you explain it more

[PoGibas]

If your input into bedtools genomecov is a bam file, then you have to use -ibam. And if your input is a bed file, then you have to use only -i.

[Azhar]

But I have unsorted bam and sorted bam.bai file which is to use

[PoGibas]

samtools sort unsorted.bam sorted.bam
genomecov -ibam sorted.bam -g hg19

bam.bai isn't bam file (Bam And Indexed Bam Files)