extract discordant,split reads from BAM file

Question

[9521ljh]

DNA sequencing data

i want to identify the sequence of fusion gene.

for example, some fusion algorithm gave me A(gene) and B(gene') are fusion.

Thus, i use the samblaster which input is BAM file and the output gave me discordant.sam file

(e.g.)

HWI-ST482:143548235:C2TWGACXX:4:1215:5836:43786 145 9   66784609        0       100M    =       66784611        -98     CTCCTTCGTTGGAAACGAGAGTATTTTCACTTAAACACTAGACAGAAGCATTCTCAGAAACTAATTTGTGATGTGTGCATTCAACTCACAGAGTTCAACC    DB@BD@B>3EDDFFEHHJJGJJJJHHEC=GGJHGCIIIIGHEIJIIIHAEHDHCFJIIHGIJJJJJJIIIHCJGIIIIHBIJIHIJIFHHHHDFFFF@C@ RG:Z:2893812918 PG:Z:2893812918 XT:A:R  NM:i:2  SM:i:0  AM:i:0  X0:i:2  X1:i:0  XM:i:2  XO:i:0  XG:i:0  MD:Z:0G0G98     XA:Z:9,-69977247,100M,2;
HWI-ST444:143456288:C2U55ACXX:5:1308:19664:33640    81  13      69979245        37      100M    =       69979245        -100    TGGACTTTCTGAATGTAATAGTTAACTGGTTCTTCAATTGTTTTAATAAAACCTTTCTCATTCAAATTCATTTTAAAGATTCAAACAGGAGTTTAAACAG    ECC@EEFFDFFFFHHHHHHHJJIJJJJJJJJIGIIJJJJIIJIIIIGHHFBHGJJJJJJJJJJJJJJJIJIHGJJJJJJJJIHIHJJHHGHHFFFFFCBB RG:Z:2893805527 PG:Z:2893805527 XT:A:U  NM:i:0  SM:i:37 AM:i:37 X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
HWI-ST444:143456288:C2U55ACXX:5:1308:19664:33640    161 13      69979245        37      100M    =       69979245        100     TGGACTTTCTGAATGTAATAGTTAACTGGTTCTTCAATTGTTTTAATAAAACCTTTCTCATTCAAATTCATTTTAAAGATTCAAACAGGAGTTTAAACAG    CCCFFFFFHHGHHJJGHIJJJIJJJJJJJHCHIJJIJIIJ@GHJIJJJIIIIJIJIIGIJJIJJIJJGJJIIJIIIJHIIJIJJJJGHHFFDFFEFEEEE RG:Z:2893805527 PG:Z:2893805527 XT:A:U  NM:i:0  SM:i:37 AM:i:37 X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100

But how to know this reads are mapped to A(gene) and B(gene')

[GenoMax]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

Answer 1

[h.mon]

You may want to look at the bedtools intersect documentation.