Changes

GotCloud: Variant Calling Pipeline (view source)

597 bytes removed , 09:27, 2 April 2013

m

Line 125: Line 125:

HM3_PREFIX = /path/reference/hapmap3_r3_b37_fwd.consensus.qc.poly ### HapMap variants

DBSNP_PREFIX = /path/reference/dbsnp_129_b37.rod ### dbSNP variants

−

~~Here's the same configuration file but made to run on a cluster computer with MOSIX.~~

−

~~CHRS = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22~~

−

~~BAM_INDEX = /path/freeze5/freeze5.bam.index~~

−

~~OUT_DIR = /path/freeze5/output~~

−

~~REF = /path/reference/hs37d5.fa~~

−

~~INDEL_PREFIX = /path/reference/1kg.pilot_release.merged.indels.sites.hg19~~

−

~~HM3_PREFIX = /path/reference/hapmap3_r3_b37_fwd.consensus.qc.poly~~

−

~~DBSNP_PREFIX = /path/reference/dbsnp_129_b37.rod~~

−

~~BATCH_TYPE = mosix ### Specify MOSIX as the batch system~~

−

~~BATCH_OPTS = -j10,11,12,13 ### Specify available MOSIX compute nodes~~

= Running =

235

edits