pd3
commented
6 years ago There is the mpileup -d option, maybe it needs increasing? Previously this limit was increased automatically with few bams.
Open agoyer opened 6 years ago
pd3
commented
6 years ago There is the mpileup -d option, maybe it needs increasing? Previously this limit was increased automatically with few bams.
agoyer
commented
6 years ago I ran mpileup with a single BAM file. I tried the option -d you suggested, set it at 1000000, but no luck. I am working on Arabidopsis, 5 chromosomes plus mitochondrial (Mt) and plastidial (Pt) genomes. I noticed that on chromosomes 1 through 5, the read depth is very low as I indicated previously, but on the other hand the read depth on Mt and Pt is very high (most often >600).
pd3
commented
6 years ago I can't think of a good reason. Could you create a small text case by extracting a small region using samtools view?
agoyer
commented
6 years ago Below is the depth on a region of chromosome 1 from one of the BAM files and the output from bcftools mpileup/call in that same region. Further below is the same region from samtools view.
[Linux@waterman bowtie2]$ samtools depth -r 1:87282-87331 rsr4.mapped.sorted.bam 1 87282 121 1 87283 121 1 87284 121 1 87285 117 1 87286 116 1 87287 118 1 87288 118 1 87289 118 1 87290 118 1 87291 118 1 87292 118 1 87293 119 1 87294 121 1 87295 119 1 87296 120 1 87297 121 1 87298 122 1 87299 126 1 87300 126 1 87301 127 1 87302 127 1 87303 127 1 87304 127 1 87305 127 1 87306 125 1 87307 125 1 87308 125 1 87309 126 1 87310 126 1 87311 129 1 87312 127 1 87313 127 1 87314 127 1 87315 126 1 87316 126 1 87317 128 1 87318 129 1 87319 132 1 87320 132 1 87321 132 1 87322 133 1 87323 132 1 87324 132 1 87325 132 1 87326 131 1 87327 130 1 87328 130 1 87329 130 1 87330 134 1 87331 131
1 87282 . A T 85 PASS DP=3;VDB=0.192436;SGB=-0.511536;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,2,1;MQ=42 GT:PL 1/1:115,9,0 1 87304 . T A 78 PASS DP=3;VDB=0.192436;SGB=-0.511536;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,2,1;MQ=42 GT:PL 1/1:108,9,0 1 87306 . A G 85 PASS DP=3;VDB=0.192436;SGB=-0.511536;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,2,1;MQ=42 GT:PL 1/1:115,9,0 1 87317 . C G 85 PASS DP=3;VDB=0.192436;SGB=-0.511536;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,2,1;MQ=42 GT:PL 1/1:115,9,0 1 87331 . A G 78 PASS DP=3;VDB=0.192436;SGB=-0.511536;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,2,1;MQ=42 GT:PL 1/1:108,9,0
[Linux@waterman bowtie2]$ SGE_Batch -c "/local/cluster/bin/samtools view rsr4.mapped.sorted.bam 1:87282-87331" -o view.rsr4.out -P 4 J00107:180:HV3NFBBXX:2:1211:25702:41598 81 1 87281 40 151M Pt 95004 0 ATATATCGTGATCCTAGATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATAC JJJFAFF<7-<JF-JJJAJFJJAFF7JJJJJJJJJJJJJJ<FJJJFJJJFJJJFJJJJJJFJF<AJJ7AFJ<JJAJFFFJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA AS:i:-27 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:1A21T1A10C13A100 YT:Z:UP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1211:25834:41651 81 1 87281 24 151M 4 5279633 0 ATATATCGTGATCCTAGATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATAC JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJFJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:1A21T1A10C13A100 YS:i:-37 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1223:1783:46715 81 1 87281 42 151M Pt 56976 0 ATATATCGTGATCCTAGATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATAC --F<-7<--7-7F77<<JAAA7FJF<FJAAAA--F--AAAA--A-FA77<JJJFFJJAF-JF-AJAJJJJJFJJA7AJAAJJJJJJJJJJFJJJJJJJJJJJJJJFJJJFFJJFJJJJJJJJJJJJJJJJJAAJJJJJJJJJJJJJFFFAA AS:i:-22 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:1A21T1A10C13A100 YS:i:-4 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1223:1753:46768 113 1 87281 42 151M Pt 9560 0 ATATATCGTGATCCTAGATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATAC JJFFF7AF77AA--AAJJFJJJJJJJJ<JJJAAFJJFF-JJFFFAFAFF<7FJFAA-JFF<F<JJAJFJJJFJJAJFF7FJJJJJJJFJJJJJJFJJJJJFFJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJFJJJJJJJFFFAA AS:i:-27 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:1A21T1A10C13A100 YS:i:-7 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1223:1570:46979 113 1 87281 3 151M = 27588136 27501007 ATATATCGTGATCCTAGATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATAC F<-7-7--7FF<F-<A-JJFJAJJJFJJJJJFJJJJJFJAJJJJJJF77A7JJJJJJJJJJJJJJJJFJJJFFA-<JJFJJJJJJJFJJJJJJJJJFJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFAA AS:i:-25 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:1A21T1A10C13A100 YS:i:-86 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2118:30360:27338 145 1 87281 42 151M Pt 62888 0 ATATATCGTGATCCTAGATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATAC A7JFJA77<<-7<AAAA<-AFFFAF7--JF<<77JFJJF<--AJF<<<J7-F<FA<AFAJJ<<JFAFAFA7FF7--AFJF--7FJJF7<JJJAJFJJJJJ<AFF77-FFF--AJFA-FJ77FJJJFJAFAJAJJ<-7FJAFJJJJFF<AAA AS:i:-22 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:1A21T1A10C13A100 YS:i:-12 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2118:30350:27356 177 1 87281 42 151M 2 14563822 0 ATATATCGTGATCCTAGATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATAC <JJJAA<JFF<AFAJAFJJFJJJJJF-AF<FFFJJ<FA-JJJJAFAFF7FFJFJJAFJJJJJJJJJJFJFFFJFFJJFJFJFJJJJJJJ<FAFFJJJJJJJJJJJ<JFJFF<JJJJJJJFAFJAJJJFFJFJA<7-JJFJ-JJJJJFFFAA AS:i:-27 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:1A21T1A10C13A100 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2103:2828:34037 177 1 87287 40 151M Pt 87436 0 CGTGATCCTAGATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACA A<JJJJJJJFFJJJJJJJAJFF<<FFAFAJJJF<JJJJJJJFFJFFJJJJJJJJJJJJJJJJJJJFJJFJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFF<JFJJ<JJJJJJJJJJAFFFAA AS:i:-23 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:17T1A10C13A106 YT:Z:UP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2103:2747:34073 177 1 87287 40 151M 2 2508334 0 CGTGATCCTAGATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACA AA<AF-AJFAFF7AAF-7FFFAAJJ<-<FJFAJJJAF<F<77FFAJJJFFJJJJJJJJJJJJJJFFJJJJJJA-JF-JF<FJJJJJJF<JJJJJJJFJFJJJJJJJJJJJJFJJJFJJJFJJJJJJJJJJJJJJJJJJJJJJJJFFA<FAA AS:i:-19 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:17T1A10C13A106 YT:Z:UP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2224:24261:15117 81 1 87293 42 151M 3 3925852 0 CCTAGATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATA JJJJJJJJJJJJJJFFJFJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA AS:i:-23 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:11T1A10C13A112 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1118:22495:46979 65 1 87294 42 151M Pt 74947 0 CTAGATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATAC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJFJJJFJJJJJJJJFJJFJAFJAJJJJJJJFJAAAAAFFJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJF AS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:10T1A10C13A113 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1118:22374:47155 97 1 87294 8 151M 5 11685396 0 CTAGATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATAC AAAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJFJJJJJJJJFJJJJJJJJJJJJ<JJJJJJJJJJJJJFJJJJJJJJJJJJJAAFJJJJJJJJJA AS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:10T1A10C13A113 YS:i:-77 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1126:29873:7433 161 1 87294 42 151M 2 13783204 0 CTAGATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATAC AAFFFJJJJJJJJ<<AJJ7AFJJJAAJ-FFAJFFJJJJAAF7AJFFJ-JJ-A-JAJJJJJJFA-FF-AJJ<<J7-<FJJJJAAAFJJ<JJJJ<AJFAJ<F7AAJJJJFJA-AA--<7AFJF-<AFAFJAAFAFF<AF<<A-FFF<F7AFJA AS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:10T1A10C13A113 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2225:15108:31927 97 1 87296 42 151M 5 16834543 0 AGATAATAAAGCGAAATTCTAGTCTAGTTTATATTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACAT AAAFAJJJFJF7AFFFFFJJ--AAJ7FFJJJF<FFAF<JFJJA-F-<-<AF-FJJJJF--7FA-<-<--7F-F<F-<A-<7<7<JA-FFJ-<AJJ<JFA7--7FA---7<-7FJAFJFJ-FFJ77-A<A<J-AAJA<AFJAJJJFJFFAJJ AS:i:-22 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:8T1A10C10T2A115 YS:i:-5 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2225:14884:31962 65 1 87296 42 151M 2 17182790 0 AGATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACAT AAFFFJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJJJJJFAAFF<FJJJJJFJJJJJFJJJJJJJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJF7 AS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:8T1A10C13A115 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2114:2656:42108 177 1 87297 40 151M 3 13589158 0 GATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATA -77JFAJJAFAAJJFJAJJJAAFJJJFJJJJJFFJJJJJJJJJJJJJJJJJJJJJJFFJFFJAAFJFJJJJJJJAJJ7AFJFJJFFJJJJJJJJJJJJJFJJJJJJA<JFFJJFFJJFFAJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA AS:i:-22 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7T1A10C13A116 YT:Z:UP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2122:2402:19584 113 1 87298 40 151M 2 3497315 0 ATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAGTATACGCAACATTTATACATAT FJJJJFFFF7FFAFJAFFFJJFJJFJJJJJFJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJF7JJJJJJJJJJJJJJJJJFFFAA AS:i:-26 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:6T1A10C13A94A22 YT:Z:UP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2208:5558:26248 81 1 87298 42 151M Pt 20328 0 ATAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATAT JJJJJJJJJJJJJFJFJJJFFJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA AS:i:-22 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:6T1A10C13A117 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1104:10348:19847 145 1 87299 42 151M 5 1686202 0 TAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATT JJFJJJJJJJJJJJJJJFJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA AS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:5T1A10C13A118 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1227:19116:14326 177 1 87299 42 151M = 1244749 1157601 TAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATT JJJJJJJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJFJJJJFJJJJJJJJJFFFAA AS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:5T1A10C13A118 YS:i:-12 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1227:19025:17157 177 1 87299 42 151M Pt 2136 0 TAATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATT AJJJJJJJJJJJJJJJJJJJJFJJJJFJJFFJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJFJJJJJJJJJJJJJJJFJJJJJJJJJFFJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJFJJJJJJJJJFFFAA AS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:5T1A10C13A118 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2204:2818:31664 145 1 87299 24 151M 5 5765877 0 TAATAAAGCGAAATTCTAGCCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATT -<A<-7-JFFJ<<-7A--)-J7AFF7A7FFAA7-<J<<AFFA--F<F-F-JF7FFFA---<-A7JJJAFJFJJJFF<AAJ<A-J<AF77<-JJ<AJJAJFAJJJJJFA-F<-FAA<-AA<JJJJJA7JFJJJ<JJJFJJFFJJJJJFFA<- AS:i:-19 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:5T1A10C0T12A118 YS:i:-40 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2103:18030:35233 145 1 87301 40 151M 4 3366796 0 ATAAAGCGAAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTT JJJJFF<JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJF<AFJJJJJJAJJJJFJJFJJJJJJJJJJFFFAA AS:i:-23 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:3T1A10C13A120 YS:i:-23 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2214:22668:22872 65 1 87309 42 151M 5 24777186 0 AAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJFFJFFFFJJJJJJFJFFFJJJFFAFJ-AJFJ<FJJJJAJ-JA7<JJAFFFFJJJJJFJFA<<FA<FFJJJ AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:8C13A128 YS:i:-13 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2214:22323:23434 97 1 87309 42 151M Pt 11493 0 AAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJFJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJFFJJJJJJFJ AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:8C13A128 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2214:22353:23487 97 1 87309 40 151M 2 689973 0 AAATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJFJJJJJJJFFJJJJJ<FFAFJJJJJFFJJFJJJJJJJFJJJJJJJ7FJJJJJJJJJJJJJJJJFJJJJJJJJJ AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:8C13A128 YS:i:-38 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1214:28737:23223 97 1 87311 42 151M 4 3709321 0 ATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJ AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:6C13A130 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1214:28838:23364 97 1 87311 42 151M Pt 334 0 ATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJAJJJFJJAJJJJJJJJJFJJJJJJF<JJJJAJFFAJFJAJFFJAAAFA<FFJJJJJJFJFJJJJJJJJJJJJJJFAJJJFJJJJJJJJJJJJJJJJFJJJJJJJJ AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:6C13A130 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1203:4848:23610 177 1 87311 8 151M 5 4217446 0 ATTCTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAA FJJFJJJJJAAJJFJJJFAJJFFFJFJFJJJJJJJJJJJJJFJFFJJJJFJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJFAJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJFFFAA AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:6C13A130 YS:i:-84 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2125:7882:18107 81 1 87314 42 151M 5 12674549 0 CTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAAATA 7JJFJJJFFJJJJJJJJJJJJJJJJJJJJFAJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA AS:i:-11 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:3C13A133 YS:i:-19 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2225:13098:28657 177 1 87314 24 151M 4 3987458 0 CTAGTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAAATA FJJJJAJJJAAFJAAJJJJAA7<JJJFFFFFAFJJFFF<JFJJJJFFJJFJAJJJJJFJJFJFF<FJJJJJJJFJJJJJFJJJJJJJJJFFJJJJJJJJJJJJJJJJFJJJJJJJJJFJJFJJAJJJJJFFAJJJJJJJJJJJJJJ<FFAA AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:3C13A133 YS:i:-54 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1108:29447:22204 177 1 87317 42 151M 5 5781627 0 GTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAAATAATA --AAJAJJJFFFAJAFJFFJJFFFFFFF<AAA<JFFFFFF7AJFFF-AFJJJJ<-JJJJJAJJJFJJJJJJJFA<F<FFFJJAAJJJJJAJJJFJJJJFFJJAJJJJJJJJFJJ<FF-<FJJJJFJFJJJJJJJJJFAJJA<FJJJFFFAA AS:i:-8 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:0C13A136 YS:i:-14 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2115:3762:21201 113 1 87317 42 151M 4 9530498 0 GTCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAAATAATA 7JJJFJJJJJJFFJAJJJJJJJJJJJJJJJJJFFFJJJAJ7<JJJJJJJJJJJJJJJJFJJJJJFJJJJJJJJJFJFA<JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA AS:i:-9 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:0C13A136 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2219:15777:24823 113 1 87318 42 151M 3 80516 0 TCTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAAATAATAT FFFJJJJJJJJJF<JJJJJJJJJFJFJJJJFJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA AS:i:-4 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:13A137 YS:i:-6 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2108:22171:35303 113 1 87319 42 151M 2 10193 0 CTAGTTTATTTTGACATTTAATTTGTATACAAATCGGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAAATAATATG FFA---FFA<7<FFJJJ<-JFJAFFJFAJJJJJFA-FJFF7FF<<JFJJJJFJJJJJJJFJJJF7JJAFJFJFJ-JJJFAJJJF<JJFJJJJAJJAAJJFFJJJJJFJAJFJJF<JFF-FJFJJJJJJJJJJJFFJJ<F<JFJJFJFFFAA AS:i:-8 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:12A22T115 YT:Z:UP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2108:22495:37765 81 1 87319 42 151M Pt 79212 0 CTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAAATAATATG FJJJJJJJJJJFJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:12A138 YS:i:-6 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2108:22577:37835 81 1 87319 42 151M 5 2179836 0 CTAGTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAAATAATATG JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:12A138 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:2220:10257:17896 161 1 87322 42 151M Pt 121970 0 GTTTATTTTGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAAATAATATGAAA AAAFFJJJJJJJJJJJJJJJJJ<JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJFFJJFJJJJJJFJJJJJJJJJJJAFFFFFF<<JJJ AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:9A141 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1103:15311:9807 65 1 87330 42 151M 5 22332853 0 TGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAAATAATATGAAAAAACGATA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJAJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJ<AJJFJJJJJJJJJJJJJJJJJJJFJJJ AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:1A149 YS:i:-6 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1103:15818:9983 97 1 87330 42 151M = 25328796 25241617 TGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAAATAATATGAAAAAACGATA A<AFFJFJJJJJJJJJJJFAJJJJJ<FFJJJJFAFJJJJJJJJJJJFJFFJJFJJ<JJJJFJJJJJJJJJJJJAF<AAJJJJJJJJFJJJJJJJJAJJJFJJ7JFJJA-7FJJJJJJJ<FJFJJJJFAFJJJJ<F<-AFFAFFJJJJJJJF AS:i:-4 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:1A149 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1103:15260:10352 65 1 87330 42 151M 5 17024998 0 TGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAAATAATATGAAAAAACGATA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJAJJJFFJJJFJF7AJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJFAJJJAJJJJJJJJJJJJJJJJJJJJJJJJJJ AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:1A149 YS:i:0 YT:Z:DP RG:Z:rsr4 J00107:180:HV3NFBBXX:2:1103:15645:10422 65 1 87330 42 151M Pt 125050 0 TGACATTTAATTTGTATACAAATCTGAGATTCAGCTATAAAGAATTATCAATGTAAGACTGCAATTTCTTCGCTCTTTAATTAATGCAAAACAAAAATATACGCAACATTTATACATATTTTATCAAGAAAAATAATATGAAAAAACGATA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJFJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:1A149 YS:i:-17 YT:Z:DP RG:Z:rsr4
pd3
commented
6 years ago That's nice thank you, but I meant a tarball with something reproducible. This is not helpful by itself.
agoyer
commented
6 years ago Sorry, I am not sure I understand what you need (I am relatively new to biocomputing). Do you want me to send you .gz files of regions of several BAM files extracted with Samtools view?
pd3
commented
6 years ago Yes. It would be very helpful if you could extract a small portion of the BAM file, the reference, and the commands to reproduce the behavior, and create a tarball (tar -czf test.tgz dir-with-the-testing-data/).
I am running bcftools mpileup (bcftools Version 1.9) on BAM files generated with Bowtie2 followed by bcftools call. The values reported under INFO DP are not correct. Most DP values show 1 or 2, and up to 7, although I know from samtools depth that these values should be much higher. Has anyone encountered this issue before?