Hi
I try to use DepthOfCovareage. My command line is
java -jar GenomeAnalysisTK.jar
-T DepthOfCoverage
-L 5:125921513-125923713
-o test
-I input.bam
-R hg18.fa
For the firsts lines I obtain these results :
Locus Total_Depth Average_Depth_sample Depth_for_N/A
5:125921513 253 253.00 253
5:125921514 285 285.00 285
5:125921515 292 292.00 292
5:125921516 310 310.00 310
5:125921517 319 319.00 319
5:125921518 320 320.00 320
(...)
but when I'm looking for the reads aligned at the position 125921513 (for example ... first line of my output file from GATK) via this command line :
samtools view input.bam | cut -f 3-4 | grep 125921513 | wc -l
I obtain 7214 data (and all of them are within chromosome 5!)
When I do the same position 125921514, I obtain 41 reads.
I'd like to understand the difference between my interpretation of the bam file and the interpretation done by GATK. Which one is good? If it's GATK what about my command line output? What does GATK use?
THanks a lot for your time
I try to use DepthOfCovareage. My command line is
java -jar GenomeAnalysisTK.jar
-T DepthOfCoverage
-L 5:125921513-125923713
-o test
-I input.bam
-R hg18.fa
For the firsts lines I obtain these results :
Locus Total_Depth Average_Depth_sample Depth_for_N/A
5:125921513 253 253.00 253
5:125921514 285 285.00 285
5:125921515 292 292.00 292
5:125921516 310 310.00 310
5:125921517 319 319.00 319
5:125921518 320 320.00 320
(...)
but when I'm looking for the reads aligned at the position 125921513 (for example ... first line of my output file from GATK) via this command line :
samtools view input.bam | cut -f 3-4 | grep 125921513 | wc -l
I obtain 7214 data (and all of them are within chromosome 5!)
When I do the same position 125921514, I obtain 41 reads.
I'd like to understand the difference between my interpretation of the bam file and the interpretation done by GATK. Which one is good? If it's GATK what about my command line output? What does GATK use?
THanks a lot for your time
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