Do I need to provide the Illumina's target region bed file for qualimap?

Question

[bioinforesearchquestions]

Hi friends,

I have trio exome sequencing data with me. In order to know the coverage for trio samples. I used qualimap tool. Why is the mean coverage very low only 5.3X. Generally, exome sequencing have 80-100X coverage right. I didn't provide the reference file for the tool. Do I need to provide the Illumina's target region bed file?

• This is the command I used

qualimap bamqc -bam sample1.bam -nt 8 sample1.bamqc -outformat PDF --java-mem-size=4G

• Output:

Reference size: 3,137,161,264 bp

Number of contigs: 93

Number of reads: 131,279,965

Mapped reads: 131,082,678 (99.85%)

Unmapped reads: 197,287 (0.15%)

Duplication rate: 57.68%

Mean Insert size: 188

Chromosome stats:

Answer 1

[igor]

You didn't give it a list of targets, so it calculated genome-wide coverage. From the SD, you can see that there are some regions that have much higher coverage.

How can it calculate on-target coverage if you don't give it the targets?

Answer 2

[trausch]

I don't have any experience with qualimap but the on-target rate and the targeted sequencing coverage can also be computed by Alfred (disclaimer: my own tool).

Answer 3

[Raony Guimarães]

You need to provide a bed file with the target regions specific to your exome target kit or you can use a generic with the official list of exome regions from UCSC.

[igor]

It depends on your question. If you want to know how well the capture worked, then you should use the regions that are designed to be captured. If you want to see if specific genes are captured, then you should use a BED file for those genes (just be careful to not include introns).

[bioinforesearchquestions]

Hi guys,

I have a query, if I have a low-pass sequenced whole genome data. Should I need to give UCSC bed file or no need of it?

I downloaded the exome interval file from the sequencing kit website. After using the exome interval file, the mean coverage is 224X.

">>>>>>>" Coverage

 mean coverageData = 224.4677X
 std coverageData = 328.406X

 There is a 99.6% of reference with a coverageData >= 1X
 There is a 99.47% of reference with a coverageData >= 2X
 There is a 99.21% of reference with a coverageData >= 3X
 There is a 99.04% of reference with a coverageData >= 4X
 There is a 98.8% of reference with a coverageData >= 5X
 There is a 98.61% of reference with a coverageData >= 6X
 There is a 98.36% of reference with a coverageData >= 7X
 There is a 98.14% of reference with a coverageData >= 8X
 There is a 97.9% of reference with a coverageData >= 9X
 There is a 97.67% of reference with a coverageData >= 10X
 There is a 97.41% of reference with a coverageData >= 11X
 There is a 97.17% of reference with a coverageData >= 12X
 There is a 96.91% of reference with a coverageData >= 13X
 There is a 96.67% of reference with a coverageData >= 14X
 There is a 96.4% of reference with a coverageData >= 15X
 There is a 96.14% of reference with a coverageData >= 16X