How to interpret bedcov tools output?

1

Hello. I would like to ask there I can find some information how to interpret BedCov tool output, because there is just numbers in the first line (header) and I can’t understand which column shows me sequence coverage? The second question is how I can visualize the coverage using Galaxy? Is there any tool which might help to do that?

2

Hi, did you find out what the bedcov output meant?

3

Hi @amyhouseman,
bedcov reports the total number of reads in the specific interval (sum of per-base read depths per BED region, discussed here). What is your goal? If you are interested in computing the average coverage of specific intervals, I suggest you to use bedtools Genome Coverage.

Regards

4

Hi! Thank you for your reply.

I wanted to work out the average read depth at each position using the bam file against the capture exome bed file - I did this using the average of the samtools depth output.

Then I want to see how much coverage and % mapping has been achieved over the capture exome bed file - for this I have just been using samtools flagstat (samtools view -bu -L capture.bed in.bam |samtools flagstat).

I think the output of this gives me what I need for the % mapped to the bed?:

91223463 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
11162 + 0 supplementary
0 + 0 duplicates
91220169 + 0 mapped (100.00% : N/A)
91212301 + 0 paired in sequencing
45644366 + 0 read1
45567935 + 0 read2
90959524 + 0 properly paired (99.72% : N/A)
91204491 + 0 with itself and mate mapped
4516 + 0 singletons (0.00% : N/A)
154458 + 0 with mate mapped to a different chr
143066 + 0 with mate mapped to a different chr (mapQ>=5)

I have ran bedcov but I don’t know if its output is relevant for the coverage mapping percentage. I did try and use bedtools genome coverage but couldn’t work out how to use my bed file as the comparison - if that makes sense!

Thanks,
Amy

5

Indeed bedcov is not relevant at all in that case; regarding bedtools genome coverage, you could use bedtools Intersect intervals in order to get the reads that overlap with the exome capture bed file, and then using it as input for the bedtools genome coverage tool.

Regards