What file from the GATK DepthOfCoverage should be input to gatk_coverage_to_bed?

[lakhujanivijay]

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]

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