Hallo everyone,
This has been bugging me for a few days now, I get empty output from bam2cfg.pl from my merged bam file. I've seen many threads but non of them helped me fix my problem. I have a merged bam file (merged with picard-tools) consisting out of 4 paired end samples of the same individual. The following command has no output:
$ perl bam2cfg.pl testdata.newbam.bam > break.cfg
My bam files looks like this:
Can anyone tell me how to fix it so bam2cfg.pl will work?
This has been bugging me for a few days now, I get empty output from bam2cfg.pl from my merged bam file. I've seen many threads but non of them helped me fix my problem. I have a merged bam file (merged with picard-tools) consisting out of 4 paired end samples of the same individual. The following command has no output:
$ perl bam2cfg.pl testdata.newbam.bam > break.cfg
My bam files looks like this:
Code:
@HD GO:none VN:1.4 SO:coordinate @SQ SN:chrM LN:16569 @SQ SN:chr1 LN:249250621 @SQ SN:chr2 LN:243199373 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 ... @SQ SN:chrUn_gl000248 LN:39786 @SQ SN:chrUn_gl000249 LN:38502 @RG ID:testdata1 DS:tumor LB:lib PG:picard-tools PI:455 PL:illumina PU:bar SM:testdata @RG ID:testdata2 DS:tumor LB:lib PG:picard-tools PI:455 PL:illumina PU:bar SM:testdata @RG ID:testdata3 DS:tumor LB:lib PG:picard-tools PI:455 PL:illumina PU:bar SM:testdata @RG ID:testdata4 DS:tumor LB:lib PG:picard-tools PI:455 PL:illumina PU:bar SM:testdata @PG ID:bwa PN:bwa VN:0.5.9-r16 FCC15WDACXX:1:1101:17486:12062 145 chrM 19 37 90M chr10 44192200 0 CTATTAACCCCTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGA CDDA85&52(B?><5BCCDBBDDCBCCCDDCBDCDDCCDBDCDCB=DHJJJJIGIJHGFGGHIGIGGGJJIIHEGIIHGHHHFFFFFCCC RG:Z:testdata1 XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:9A44A35 FCD1CR7ACXX:5:1101:18187:12124 113 chrM 22 37 90M chr2 198540778 0 TTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGAGAGCATTGCGAGACGCTGGAGCCGGAGCA C@<3?:+?8B?BBCCC@@=DDA>D@DC>BCCDDCCDB=88=9A6DHJJIIGIHGG@GHDFD9GGIGIGFCIGIGJJJHHHHHFFFFFCCC RG:Z:testdata2 XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:51A9T28 FCD1CFTACXX:5:1101:7853:10375 65 chrM 30 37 90M chr18 33913273 0 TCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGT @B@DDDDDF<DFHIGAFEFEHIIG>B?EGE9D@FGIJIGIIB@B8<>CCB8@8-7<CDDCCA;-88885@B@AA?B@59<<<ABD83AC: RG:Z:testdata3 XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:43A46 FCD1CR7ACXX:5:1101:14274:9671 113 chrM 64 37 90M chr13 34187260 0 CTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCTCA <<DDDBBBCCA<90BBBDDCDDCBDCBCEFDBGHFIIIGGHIIHFHD;JIEJJJIGGIJJJJGIIJJJIJJJJJJIJHHHGHFFFFFCCC RG:Z:testdata4 XT:A:U NM:i:3 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:9A77C0T1