This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
readme.illumina2pregs [2019/09/27 00:36] ignacio [Input files] |
readme.illumina2pregs [2020/12/09 16:57] (current) ignacio [Output files] |
||
---|---|---|---|
Line 27: | Line 27: | ||
<file>--genome</file> | <file>--genome</file> | ||
Indicate type of genome (1 - bovine, 2 - ovine) | Indicate type of genome (1 - bovine, 2 - ovine) | ||
- | <file>--nosortmap</file> | + | <file>--sortmap</file> |
- | Genotype file will be in the same order as given | + | Genotype file will be sorted by chromosome and position |
<file>--gc <thr></file> | <file>--gc <thr></file> | ||
Set GC cutoff (thr) for exclude call (default from GenomeStudio 0.15) | Set GC cutoff (thr) for exclude call (default from GenomeStudio 0.15) | ||
Line 34: | Line 34: | ||
Set the maximun length to store alphanumeric IDs (default 10) | Set the maximun length to store alphanumeric IDs (default 10) | ||
<file>--snpfile_out</file> | <file>--snpfile_out</file> | ||
- | Set a file name for output SNP file (default snps2pregs) | + | Set a file name for the output of the SNP file (default snps2pregs) |
+ | <file>--mapfile_out</file> | ||
+ | Set a file name for the output of the MAP file (default snp_map) | ||
=====File formats===== | =====File formats===== | ||
Line 78: | Line 79: | ||
''snp_map'' | ''snp_map'' | ||
- | 1 index | + | 1 name |
2 chromosome | 2 chromosome | ||
3 position | 3 position | ||
- | 4 name | + | 4 index in original SNP_Map.txt |
- | 5 index in original SNP_Map.txt | + | |
SNP without defined position (CHR = 0) in the SNP_Map.txt will be located in a new CHR 32 in the output snp_map, but still with 0 position. | SNP without defined position (CHR = 0) in the SNP_Map.txt will be located in a new CHR 32 in the output snp_map, but still with 0 position. |