Homozygous deletion of region 5,137,301 to 5,139,463 from chromosome X.

Currently compatible with GenomeSTRiP discovery & CNV output.

Wrapper extract_regions.sh executes 5 steps:

1. separateTable.R

   Input: results table from either Genome STRiP pipeline
   Output: Coordinates of SVs for each sample and zygosity of SV (ref/het/hom/duplication)

   chr     start   stop    ID              len     type
   chr1    1288120 1289853 DEL_P0001_56    1317    hetDel
   chr1    1934917 1935701 DEL_P0001_156   782     hetDel

2. readBamChunks.go

   Output: Table of coordinates and extra information of reads aligned to SV +/- 1.5kb

   HX3_17636:5:2216:22901:43097_1  chr1    1277812 1277963 -424    22M1I128M   60  AS:i:133    pP--r-1-----
   HX2_17657:5:1212:17421:67217_1  chr1    1277819 1277970 -655    151M        60  AS:i:151    pP--r-1-----
   HX7_17624:5:2213:2757:52608_1   chr1    1277830 1277981 0       23M128S     0   AS:i:23     p----R-2----
   

3. assignBins.R

   Output: Same table, with appended column with height value for reads, to allow non-overlapping plotting

   name                            start       end     width   bin cigar       mapq    AS          flags           tlen
   HX3_17636:5:2216:22901:43097_1  1277812   1277963    152    1   22M1I128M   60      AS:i:133    pP--r-1-----    -424
   HX2_17657:5:1212:17421:67217_1  1277819   1277970    152    2   151M        60      AS:i:151    pP--r-1-----    -655
   HX7_17624:5:2213:2757:52608_1   1277830    1277981   152    3   23M128S     0       AS:i:23     p----R-2----    0
   

4. splitCigar.go

   Output: Converted table: from one row per read, to one row per cigar operator

   HX3_17636:5:2216:22901:43097_1  1277812 1277833 1   60  one 133 0   22M1I128M   M   22
   HX3_17636:5:2216:22901:43097_1  1277834 1277834 1   60  one 133 0   22M1I128M   I   1
   HX3_17636:5:2216:22901:43097_1  1277835 1277962 1   60  one 133 0   22M1I128M   M   128
   HX2_17657:5:1212:17421:67217_1  1277819 1277969 2   60  one 151 0   151M        M   151
   HX7_17624:5:2213:2757:52608_1   1277830 1277852 3   0   two 23  0   23M128S     M   23

5. viewRegions.R

   Output: One plot per SV, coverage and read details

There are multiple Go scripts in this repo, and Go can only manage one 'main' per directory.

Yes. Yes it does!
And yet here we are!