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calculate haloplex coverage

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

next-gen
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updated by trausch trausch • written by jonessara770 jonessara770

a few questions:

1) what is the output of

samtools view -c your.bam input "TP53chrom:TP53star-TP53end" ?

2) what was your gatk command line ? 3) did you remove the PCR duplicate like picard "Markduplicate" ?

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks 1) this command samtools view -c your.bam input "TP53chrom:TP53star-TP53end" ? gives me

22372

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

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updated by GenoMax GenoMax • written by jonessara770 jonessara770

are you sure about gene.bed (same build ?) try 

  samtools view -c -L gene.bed mybam.matefixed.sorted.bam
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written by Pierre Lindenbaum Pierre Lindenbaum

Here is the output : 22372

Do you recommend any other tools to get the coverage? thanks

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written by jonessara770 jonessara770

no idea. evrythin looks fine... all the reads have a bad quality ? are poorly mapped (orphan) ? ...

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written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

We have used Alfred to calculate Haloplex on-target rate and target coverage distribution.

alfred qc -r <ref.fa> -b <targets.bed.gz> <align.bam>

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written by trausch trausch

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