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rgcgithub / clamms

CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.
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What file from the GATK DepthOfCoverage should be input to gatk_coverage_to_bed? #18

Open lakhujanivijay opened 5 years ago

lakhujanivijay commented 5 years ago

There are multiple files created from GATK DepthOfCoverage as given below

cumulative_coverage_counts
cumulative_coverage_proportions
gene_summary
interval_statistics
interval_summary
statistics
summary

Which one from the above should act as sample.gatk_readDepth_1x_q30.out for the coverage calculation i.e. which file should be input to gatk_coverage_to_bed ?

tanlaboratory commented 4 years ago

I tried this function recently. The input should be a base level read depth file. such as

Locus   Total_Depth Average_Depth_sample    Depth_for_NA12878
1:10001 0   0.00    0
1:10002 0   0.00    0
1:10003 0   0.00    0
1:10004 0   0.00    0
1:10005 0   0.00    0
1:10006 0   0.00    0
1:10007 0   0.00    0

This file can be generated by GATK by the following command:

java -Xmx3072m -XX:ParallelGCThreads=1 -XX:ConcGCThreads=1 -Djava.io.tmpdir=./ -jar ~/gatk-3.5/GenomeAnalysisTK.jar 
-T DepthOfCoverage 
-I ~/data/CRAM/NA12878.cram 
-R ~/reference/genome.hg38rg.fa 
--minMappingQuality 30 
-o ./FILE_NAME