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Depth of Coverage -genelist

Hello friends.

I tried to generate depth of coverage on a gene-by-gene basis but was unsuccessful. I created my own RefFlat file for Mouse MM10 by mimicking you files online. I did not know what the first field was so I just made it "500."

See my commands and the header to the file below. Please note this worked to create a full depth of coverage for all base sites, and gave me some summery statistics, but unfortunately, the "gatk.depth.sample_gene_summary" file was empty.

Any advice would be appreciated!

!/bin/bash

#

$ -cwd

$ -j y

$ -S /bin/bash

REF=/home/jak53/Mouse
GATK=/home/jak53/GenomeAnalysisTK-2.1-10-gdbc86ec
JAVA=/opt/java/jdk1.6.0_26/bin
BUNDLE=/home/jak53/Bundle
BAM=/groups/rossi/bam
PICARD=/opt/picard-tools-1.63
SAMTOOLS=/home/jak53/bin

$JAVA/java -Xmx6g -jar $GATK/GenomeAnalysisTK.jar \
-T DepthOfCoverage \
-R $REF/mm10.fa \
-I $BAM/analysis2.list \
-geneList /home/jak53/cisgenome_project/mm10/refFlat_sorted.txt \
--minMappingQuality 20 \
--minBaseQuality 17 \
-o $BAM/gatk.depth

500 NR_003518 chrUn_JH584304 - 52673 59689 59689 59689 7 52673,54720,55111,55464,56985,58563,59591, 54479,54867,55248,55701,57151,58835,59689, 0 Pisd-ps3 cmpl cmpl 0,
500 NM_001037742 chr1 - 57388243 57406674 57388495 57406461 8 57388243,57390641,57391448,57393349,57394046,57396726,57401368,57406383, 57388752,57390758,57391536,57393487,57394091,57396796,57401523,57406674, 0 1110034B05Rik cmpl cmpl 0,
500 NM_001114102 chr1 - 57393320 57406674 57393450 57406461 5 57393320,57394046,57396726,57401387,57406383, 57393487,57394091,57396796,57401523,57406674, 0 1110034B05Rik cmplcmpl 0,
500 NR_004860 chr1 - 57388243 57406674 57406674 57406674 8 57388243,57390641,57391448,57393349,57394046,57396726,57401387,57406383, 57388752,57390758,57391536,57393487,57394091,57396796,57401523,57406674, 0 1110034B05Rik cmpl cmpl 0,
500 NM_026503 chr1 - 23995938 24005640 23996250 24005600 3 23995938,24003156,24005545, 23996360,24003306,24005640, 0 1110058L19Rik cmpl cmpl 0,
500 NM_026876 chr1 + 151428647 151458183 151428876 151457934 15 151428647,151433793,151435727,151439515,151440805,151442586,151443246,151448253,151449899,151452047,151453076,151453884,151454977,151457462,151457681, 151429102,151433904,151435841,151439580,151440935,151442710,151443326,151448497,151450112,151452238,151453155,151454051,151455040,151457589,151458183, 0 1190005F20Rik cmpl cmpl 0,
500 NM_025819 chr1 - 151367698 151428435 151368458 151423560 20 151367698,151370578,151372307,151379382,151384316,151388619,151391435,151394608,151397205,151401079,151402954,151403794,151405415,151407575,151410770,151412790,151420099,151422033,151423506,151428296, 151368588,151370643,151372374,151379514,151384504,151388768,151391574,151394772,151397351,151401173,151403143,151403896,151405545,151407635,151411458,151412846,151420183,151422120,151423605,151428435, 0 1200016B10Rik cmpl cmpl 0,
500 NM_024283 chr1 + 43730601 43742564 43730884 43742406 4 43730601,43737199,43738559,43742244, 43730963,43737247,43738717,43742564, 0 1500015O10Rik cmpl cmpl 0,
500 NR_033199 chr1 + 33669823 33670712 33670712 33670712 1 33669823, 33670712, 0 1700001G17Rik cmpl cmpl 0,
500 NR_040554 chr1 + 187125137 187127852 187127852 187127852 3 187125137,187125629,187127561, 187125315,187125983,187127852, 0 1700007P06Rik cmpl cmpl 0,

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