Entering edit mode
7.6 years ago
jonessara770
▴
240
Hi,
How do you calculate the coverage of target genes with Haloplex data? I am trying to use GATK but it gives 0 for TP53. However, when I check the coverage in IGV the gene is well covered...
any suggestion?
Thanks Sara
a few questions:
1) what is the output of
2) what was your gatk command line ? 3) did you remove the PCR duplicate like picard "Markduplicate" ?
Thanks 1) this command
samtools view -c your.bam input "TP53chrom:TP53star-TP53end"
? gives me22372
2)
java -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R Homo_sapiens.GRCh37.fa -I mybam.matefixed.sorted.bam -L gene.bed -o myout.genelist_coverage --minMappingQuality 15 --minBaseQuality 10 --logging_level INFO --summaryCoverageThreshold 5 --summaryCoverageThreshold 7 --summaryCoverageThreshold 10 --summaryCoverageThreshold 15 --summaryCoverageThreshold 20 --summaryCoverageThreshold 30 --summaryCoverageThreshold 50
3) I did not remove duplicate coz it is a Haloplex and it is recommended by the company to not remove duplicates
are you sure about gene.bed (same build ?) try
Here is the output : 22372
Do you recommend any other tools to get the coverage? thanks
no idea. evrythin looks fine... all the reads have a bad quality ? are poorly mapped (orphan) ? ...
How can I check these?