Open zhangrengang opened 6 years ago
The below is two examples, one within a gap and one neighbored to a gap:
$ samtools tview mapped.bam.rg.bam -p chr10:22690835 --reference ref.fa 22690841 22690851 22690861 22690871 22690881 22690891 22690901 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN CCTTTATTGATCGCACTAGCT CCTTTATTGATCGCACTAGCT cctttattgatcgcactagct $ samtools view mapped.bam.rg.bam chr10:22690856 |less E00500:171:HHYL3CCXY:1:2219:3934:66918 99 chr10 22690856 49 95S21M35S = 22690856 21 AGAACTTGCCCGCTTTGTGAGCTTTCGTAAAGTCTAGATCATCCACATCCAATGGTGAGCTACCACCTTGAGCCGGACTAGCGACCATACAAATCCCTTTATTGATCGCACTAGCTTCCGTCAAAAGATAAGCCAAACCAAATCGAGAAAG AAFFFJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ XA:Z:chr12,+27251816,87S19M45S,0; MC:Z:5S21M124S MD:Z:21 RG:Z:SR NM:i:0 AS:i:21 XS:i:19 E00500:171:HHYL3CCXY:1:2219:3934:66918 147 chr10 22690856 52 5S21M124S = 22690856 -21 AAATCCCTTTATTGATCGCACTAGCTTCCGTCAAAAGATAAGCCAAACCAAATCGAGAAAGACATTGTACTGCAAACCCACCTTCTACTGGCACAGAAGAGTCCGCAGGAGGCTTCAACTTTCCAGTAGGTGGTCCACCTTGAGTTTGAA FAFFJJJJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJFJJJFJFJJAFFJJJJJJ<JJAJJJJJJJJJJJJJJJJJ<JJJFJJJJAJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJFFFA MC:Z:95S21M35S MD:Z:21 RG:Z:SR NM:i:0 AS:i:21 XS:i:0 $ samtools tview mapped.bam.rg.bam -p chr10:22691030 --reference ref.fa 22691031 22691041 22691051 22691061 22691071 22691081 22691091 nnnnnnnnnnnnnntgtgtgcggctaacccttgtaactgagcagttaactgagcaatatgatcagcttgggcctgatgct A.................................................................. A.................................................................. A.................................................................. A.................................................................. .................................................................. .................................................................. .................................................................. ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, $ samtools view mapped.bam.rg.bam chr10:22691030 |less E00500:171:HHYL3CCXY:1:2117:27255:51096 163 chr10 22691043 59 151M = 22691098 206 ATGTGTGCGGCTAACCCTTGTAACTGAGCAGTTAACTGAGCAATATGATCAGCTTGGGCCTGATGCTCCCCCTGGCCCTCTGCAGCAGGTGCAGGCTGTTCCTCTGGAGGAGCAGCAGCAAGAGGCACATGAAGAAGATGTGCAGAAGATT AAFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ XA:Z:chr08,-14289051,151M,2; MC:Z:151M MD:Z:0C150 RG:Z:SR NM:i:1 AS:i:150 XS:i:141 E00500:171:HHYL3CCXY:1:2117:26890:51658 163 chr10 22691043 59 151M = 22691098 206 ATGTGTGCGGCTAACCCTTGTAACTGAGCAGTTAACTGAGCAATATGATCAGCTTGGGCCTGATGCTCCCCCTGGCCCTCTGCAGCAGGTGCAGGCTGTTCCTCTGGAGGAGCAGCAGCAAGAGGCACATGAAGAAGATGTGCAGAAGATT AAFAFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJFJJJJJJJJJJFJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJAJJ XA:Z:chr08,-14289051,151M,2; MC:Z:151M MD:Z:0C150 RG:Z:SR NM:i:1 AS:i:150 XS:i:141 E00500:171:HHYL3CCXY:1:2117:26474:51992 163 chr10 22691043 59 151M = 22691098 206 ATGTGTGCGGCTAACCCTTGTAACTGAGCAGTTAACTGAGCAATATGATCAGCTTGGGCCTGATGCTCCCCCTGGCCCTCTGCAGCAGGTGCAGGCTGTTCCTCTGGAGGAGCAGCAGCAAGAGGCACATGAAGAAGATGTGCAGAAGATT AAFFFJFJJAJ-FJJJFJJJJJJJFJJJFF<JJ-JJJJFJJFFF<JJJJJJJJFJFJ-<JAA<FJJFJJJJJJJJFJJ<JJFJFJJFJFJF<7FJJJJJ<AJA<<FFAFJFFJJJJJJAJFJJJJJ<A-7AFJJFFJFJJJJJAFF7FFFA XA:Z:chr08,-14289051,151M,2; MC:Z:151M MD:Z:0C150 RG:Z:SR NM:i:1 AS:i:150 XS:i:141
The version is 0.7.17-r1188 and the command is
bwa mem ref.fa R1.fastq.gz R2.fastq.gz -t 8
The below is two examples, one within a gap and one neighbored to a gap:
The version is 0.7.17-r1188 and the command is