findGCO is a Perl package for identifying gene conversion events with the next-generation sequencing (NGS) data from the two parents and their progeny in an F1 hybrid population of oubred species. It uses the usual bioinformatics tools such as bwa, samtools and picard-tools for filtering and mapping reads, phasing haplotypes of parents and genotyping each individual.
After extracting the package file, it is easy to start the process like this,
perl findGCO.plHowever, a text file named parameters.txt is needed for setting input parameters, in which some software folders and fastq files are included. It is also include parameters like THREADS(setting the number of threads to be used for computing), ALPHA(setting the maximum percentage of edit distance to a single read length in for filtering mapped reads in SAM files), MQ (mapping quality), BQ(base quality) and GQ(genotype quality). If the parental linkage maps are available, each can be incorporated in a text file formatted as follows.
LG1
Chr01 400706 a/b
Chr01 1241060 b/a
Chr01 1805157 a/b
Chr01 1881967 b/a
..................
LG2
Chr02 31567 b/a
Chr02 253351 b/a
Chr02 1014616 b/a
Chr02 1387860 b/a
.................
When the run is finished, the final results for each parent are summarized in Excel files, namely parent1GCs.xlsx and parent2GCs.xlsx, as well as parent1COs.xlsx and parent2COs.xlsxif the parental linkage maps are available. The Excel Sheets for GC results of each sample are formated as follows:
| RefSeq | 2-19bp | 20-200bp | 200bp-1kb | 1-2kb | 2-10kb | >=10kb | TotalGCs | GClength |
|---|---|---|---|---|---|---|---|---|
| Chr01 | 33 | 360 | 190 | 11 | 5 | 0 | 561 | 222.37 |
| Chr02 | 3 | 125 | 69 | 5 | 3 | 0 | 199 | 235.24 |
| Chr03 | 11 | 120 | 73 | 3 | 2 | 0 | 196 | 233.36 |
| Chr04 | 6 | 147 | 73 | 7 | 1 | 0 | 227 | 216.90 |
| Chr05 | 10 | 154 | 84 | 3 | 1 | 0 | 241 | 207.44 |
| Chr06 | 7 | 131 | 71 | 6 | 4 | 0 | 208 | 240.49 |
| Chr07 | 9 | 113 | 54 | 2 | 2 | 0 | 169 | 218.80 |
| Chr08 | 5 | 89 | 59 | 8 | 1 | 0 | 156 | 299.72 |
| Chr09 | 6 | 62 | 27 | 0 | 0 | 0 | 89 | 182.06 |
| Chr10 | 8 | 154 | 82 | 7 | 2 | 0 | 243 | 231.16 |
| Chr11 | 10 | 108 | 60 | 6 | 1 | 0 | 174 | 255.92 |
| Chr12 | 8 | 88 | 36 | 4 | 1 | 0 | 128 | 221.00 |
| Chr13 | 6 | 102 | 47 | 7 | 3 | 0 | 156 | 247.39 |
| Chr14 | 6 | 118 | 57 | 1 | 2 | 0 | 176 | 197.28 |
| Chr15 | 9 | 94 | 48 | 2 | 2 | 0 | 144 | 212.95 |
| Chr16 | 4 | 71 | 51 | 4 | 0 | 0 | 126 | 247.08 |
| Chr17 | 9 | 93 | 66 | 3 | 1 | 0 | 162 | 242.83 |
| Chr18 | 7 | 126 | 52 | 8 | 0 | 0 | 186 | 230.16 |
| Chr19 | 5 | 145 | 92 | 4 | 2 | 0 | 241 | 226.85 |
| Others | 2 | 122 | 77 | 5 | 1 | 0 | 204 | 240.44 |
| Total | 164 | 2522 | 1368 | 96 | 34 | 0 | 3986 | 229.92 |
The Excel Sheets for CO results of each sample are as follows:
| Chromosome | Start | End | Phase | Length | Discription (Mi-j:the jth SNP in linkage group i; BkMi-j: the Mi-j SNP is within haplotype block k) |
|---|---|---|---|---|---|
| Chr01 | 400491 | 21213789 | 0 | 20813299 | B1M1-1; M1-2; B2M1-3; M1-4; B3M1-5; B4M1-6; B5M1-7; M1-8; M1-9; M1-10; M1-11; B6M1-12; B7M1-13; M1-14; M1-15; B8M1-16; B9M1-17; M1-18; M1-19; M1-20; B10M1-21; M1-22; B11M1-23; B12M1-24; M1-25; B13M1-26; B14M1-27; M1-28; B15M1-29; B16M1-30; B17M1-31; B18M1-32; M1-33; M1-34; M1-35; B19M1-36; M1-37; B20M1-38; B21M1-39; B22M1-40; B23M1-41; M1-42; M1-43; M1-44; M1-45; B24; B24M1-46; M1-47; M1-48; M1-49; B25M1-50; M1-51; B26M1-52; B27M1-53; B28M1-54; B29M1-55; M1-56; M1-57; B30M1-58; B31M1-59; B32M1-60; B33M1-62; M1-63; B34M1-64; B35M1-65; M1-66; M1-67; M1-68; M1-69; B36M1-70; B37M1-71; M1-72; B38M1-73; B39M1-74; M1-75; B40M1-76; B41M1-77; B42M1-78; M1-79 |
| Chr01 | 22596858 | 39971988 | 1 | 17375131 | B43M1-80; B44M1-81; M1-82; M1-83; M1-84; B45M1-85; M1-86; M1-87; B46M1-88; M1-89; B47M1-90; B47; B49M1-92; B50M1-93; B51M1-94; M1-95; M1-96; M1-97; M1-98; M1-99; B52M1-100; M1-101; B53M1-102; B54M1-103; B54; M1-104; B55M1-105; M1-106; B56M1-107; M1-108; B57M1-109; B58; B58M1-110; B59M1-111; M1-112; M1-113; B60M1-114; B61M1-115; B62M1-116; B62; M1-117; B63M1-118; B64M1-119; B65M1-120; B66M1-121; B67M1-122; B68M1-123; B69M1-124; M1-125; B70M1-126; M1-127; B71M1-128; B72M1-129; B72; B73; B73M1-130; M1-131; B74M1-132; B75M1-133; B76M1-134; B77M1-135; M1-136 |
| Chr01 | 41107485 | 41150789 | 0 | 43305 | B78M1-137; M1-138 |
| Chr01 | 41251150 | 41251150 | 1 | 1 | M1-139 |
| Chr01 | 42007549 | 50311944 | 0 | 8304396 | B79M1-140; B80M1-141; M1-142; M1-143; B81; B81M1-144; M1-146; B82M1-147; B83M1-148; M1-149; B84M1-150; B85M1-151; M1-152; M1-153; M1-154; M1-155; M1-156; B86M1-157; B87M1-158; B88M1-159; B89M1-160 |