From Genome Analysis Wiki
Jump to navigationJump to search
190 bytes added
, 18:55, 19 March 2016
Line 388: |
Line 388: |
| -d debug [false] | | -d debug [false] |
| -q do not print options and summary [false] | | -q do not print options and summary [false] |
− | -n do not fail when REF is inconsistent with reference sequence for non SNPs [false] | + | -m exits when REF is inconsistent with |
| + | unmasked reference sequence for non SNPs. |
| + | This overides the -n option [false] |
| + | -n warns but does not exit when REF is inconsistent |
| + | with reference sequence for non SNPs [false] |
| -w window size for local sorting of variants [10000] | | -w window size for local sorting of variants [10000] |
| -I file containing list of intervals [] | | -I file containing list of intervals [] |