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Published 20 hours ago • verified publisher icon walaj

calculate SR DR through alignment file

Open thelingxichen opened this issue 5 years ago • 2 comments

Hi,

This is the alignment information for a somatic SV event.

Global BP: : 1:1,038,901(-) to 1:1,039,297(+) SPAN 396 c_1_1029001_1054001_367C  n001:0 t000:6 ins_aginst_contig 0 del_against_contig 0  c_1_1029001_1054001_367C
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>................................................................................................................      C[0,1
14] G[1039184,1039297]  Local: 1        Aligned to: chr1:1039183(+) CIG: 114M112S MAPQ: 60 SUBN 0 Disc: 1:1038873(-)-1:1039346(+) Tcount: 7 Ncount: 0 Mean MAPQ: 60 Mean Mate MAPQ: 53 Valid: TRUE  -- c_1_1029001_1054001_367C
..................................................................................................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>...........      C[114
,215] G[1038901,1039001]        Local: 1        Aligned to: chr1:1038900(+) CIG: 114S101M11S MAPQ: 60 SUBN 0 Disc: 1:1038873(-)-1:1039346(+) Tcount: 7 Ncount: 0 Mean MAPQ: 60 Mean Mate MAPQ: 53 Valid: TRUE  -- c_1_1029001_1054001_367C
ACCCCGGCCTCCTGAATAGTTGGGACCTCAGGTGCACACCATTACACCCAGGTAACGTCCTTTTCTTTTGTAGAGACTGTGTTGCCCAGGCTGGTCTCAAATGCCTGGCCTCAACACACCTGCGGTGAGCGGTGGCTCAGGTCACTGCATGGCACAGGGTGCACGCAGGGGTCAGGGGTCTGCCAGAAACGAGCGGCATCTATACACAGGACTCCCCTCGGCTCTT    c_1_102
9001_1054001_367C
ACCCCGGCCTCCTGAATAGTTGGGACCTCAGGTGCACACCATTACACCCAGGTAACGTCCTTTTCTTTTGTAGAGACTGTGTTGCCCAGGCTGGTCTCAAATGCCTGGCCTCAACACACCTGCGGTGAGCGGTGGCTCAGGTCACTGCAT                                                                            t000_161_E0
0514:191:H3YHNCCXY:4:1117:4350:58778--1:1039183 r2c CIGAR: 150M, c_1_1029001_1054001_367C
ACCCCGGCCTCCTGAATAGTTGGGACCTCAGGTGCACACCATTACACCCAGGTAACGTCCTTTTCTTTTGTAGAGACTGTGTTGCCCAGGCTGGTCTCAAATGCCTGGCCTCAACACTCCTGCGGTGAGCGGTGGCTCAGGTCACTGCAT                                                                            t000_161_E0
0516:172:H3H3YCCXY:7:1112:17929:2557--1:1039183 r2c CIGAR: 150M, c_1_1029001_1054001_367C
         TCCTGAATAGTTGGGACCTCAGGTGCACACCATTACACCCAGGTAACGTCCTTTTCTTTTGTAGAGACTGTGTTGTCCAGGCTGGTCTCAAATGCCTGG      TCACACCTGCGGTGAGCGGTGGCCAGGTCACTGCATGGCACAGGGTGCACGCAGGGGTCAGGGGTCTGCC                                          t000_83_E00
514:191:H3YHNCCXY:4:2112:27113:50779--1:1039192 r2c CIGAR: 99M28S,n001_83_E00516:197:H5MGTCCXY:7:2224:26027:37612--1:1038871 r2c CIGAR: 29S22M1D76M, c_1_1029001_1054001_367C
                               GTGCACACCATTACACCCAGGTAACGTCCTTTTCTTTTGTAGAGACTGTGTTGCCCAGGCTGGTCTCAAATGCCTGGCCTCAACACACCTGCGGTGAGCGGTGGCTCAGGTCACTGCATGGCACAGG                                                                    t000_97_E00
514:191:H3YHNCCXY:4:2116:24383:72280--1:1039214 r2c CIGAR: 127M, c_1_1029001_1054001_367C
                               GTGCACACCATTCCACCCAAGTAACGTCCTTTTCTTTTGTAGAGACTGGGTTGCCCAGGCTGCTCTCAAATGCCTGGCCTCAACACACCTGCGGTGAGCGGTGGC                                                                                          t000_65_E00
514:191:H3YHNCCXY:5:1201:31822:35766--1:1039214 r2c CIGAR: 105M22S, c_1_1029001_1054001_367C
                                                     AACGTCCTTTTCTTTTGTAGAGACTGTGTTGCCCAGGCTGGTCTCAAATGCCTGGCCTCAACACACCTGCGGTGAGCGGTGGCTCAGGTCACTGCATGGCACAGGGTGCACGCAGGGGTCAGGGGTCTGCCAGAAACGAGCGGCATCTAT                       t000_163_E0
0514:191:H3YHNCCXY:5:1112:19816:46437--1:1038900 r2c CIGAR: 150M, c_1_1029001_1054001_367C
                                                                                                   AATGCCTGGCCTCAACACACCTGCGGTGAGCGGTGGCTCAGGTCACTGCATGGCACAGGGTGCACGCAGGGGTCAGGGGTCTGCCAGAAACGAGCGGCATCTATACACAGGACTCCCCTCGGCTCTT     t000_8
1_E00514:191:H3YHNCCXY:4:1105:28260:14125--1:1038900 r2c CIGAR: 127M, c_1_1029001_1054001_367C
                                                                                                                  CACACCTGCGGTGAGCGGTGGCTCAGGTCACTGCATGGCACAGGGTGCACGCAGGGGTCAGGGGTCTGCCAGAAACG                                   n001_105_E0
0516:197:H5MGTCCXY:8:1222:3884:34834--1:1038876 r2c CIGAR: 24S101M2S, c_1_1029001_1054001_367C
                                                                                                                  CACACCTGCGGTGAGCGGTGGCTCAGGTCACTGCATGGCACAGGGTGCACGCAGGGGTCAGGGGTCTGCCAGAAACG                                   t000_99_E00
514:191:H3YHNCCXY:4:1213:13027:38051--1:1038894 r2c CIGAR: 24S101M2S, c_1_1029001_1054001_367C
                                                                                                                  CACACCTGCGGTGAGCGGTGGCTCAGGTCACTGCATGGCACAGGGTGCACGCAGGGGTCAGGGGTCTGCCAGAAACGAGCGGCATCTATA                      t000_99_E00
514:191:H3YHNCCXY:5:1219:25631:63472--1:1038899 r2c CIGAR: 11S101M15S, c_1_1029001_1054001_367C

I want to know how "Tcount: 7 Ncount: 0" is counted?

Meanwhile, the vcf record for this variation is:

chr1    1038901 6183:1  c       ]chr1:1039297]c 0       PASS    BX=ACGCCAGGTCCGAATT-1_1,TACTAGGGTGATTACC-1_1,CAACAACAGCATGACG-1_4;DISC_MAPQ=60;EVDNC=ASDIS;MAPQ=60;MATEID=6183:2;MATENM=1;NM=0;NUMPARTS=2;SCTG=c_1_1029001_1054001_367C;SPAN=
396;SVTYPE=BND     GT:AD:DP:GQ:PL:SR:DR:LR:LO      0/0:0:46:12.6:0,12.6,138.6:0:0:12.92:0  0/0:8:108:3.6:0,3.6,277.2:6:7:3.936:14.29
chr1    1039297 6183:2  a       a[chr1:1038901[ 0       PASS    BX=ACGCCAGGTCCGAATT-1_1,TACTAGGGTGATTACC-1_1,CAACAACAGCATGACG-1_4;DISC_MAPQ=53;EVDNC=ASDIS;MAPQ=60;MATEID=6183:1;MATENM=0;NM=1;NUMPARTS=2;SCTG=c_1_1029001_1054001_367C;SPAN=
396;SVTYPE=BND     GT:AD:DP:GQ:PL:SR:DR:LR:LO      0/0:0:46:12.6:0,12.6,138.6:0:0:12.92:0  0/0:8:108:3.6:0,3.6,277.2:6:7:3.936:14.29

How SR=6, DR=7, and AD=8 is calculated based on the alignment information? I didn't seen 7 discordant reads in alignment file.

Thanks a lot

thelingxichen avatar Aug 08 '18 08:08 thelingxichen

And for the read t000_161_E00514:191:H3YHNCCXY:4:1117:4350:58778--1:1039183, how come the CIGAR is 150M support the variant? Should 150M means totally match to the reference from chr1:1039183?

thelingxichen avatar Aug 08 '18 09:08 thelingxichen

Hi, A few comments that might help address your questions:

  • The size of your variant is small, only 396 bases. Depending on your insert size, what IGV "flags" as a discordant read may not be what SvABA flags. For very large variants, they should always agree, but when the variant size is near the insert size, it gets tough to say what is discordant, and what is just an outlier normal pair.
  • SR is the number of split reads as inferred from read-to-contig alignments, not necessarily what IGV shows. There should be 6 reads that sufficiently overlap the breakpoint in contig coordinates. As you discovered, the best way to look at that is the alignments file, because this is in contig coordinates.
  • The 150M in the alignments file refers to the alignment of the read to the contig, not the read to the genome. The key concept in SvABA is that there are two coordinate systems, the genomic and the contig. Variant reads will align as matches to a variant contig, and as split etc to the genome.

I hope this helps!

On Wed, Aug 8, 2018 at 5:17 AM, Paprika Chan [email protected] wrote:

And for the read t000_161_E00514:191:H3YHNCCXY:4:1117:4350:58778--1:1039183, how come the CIGAR is 150M support the variant? Should 150M means totally match to the reference from chr1:1039183?

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walaj avatar Aug 10 '18 23:08 walaj