Open lakhujanivijay opened 5 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
There are multiple files created from GATK
DepthOfCoverage
as given belowWhich one from the above should act as
sample.gatk_readDepth_1x_q30.out
for the coverage calculation i.e. which file should be input togatk_coverage_to_bed
?