v7-Genome Preparation

v0.5.0

SNPsplit_genome_preparation

• Added option --v7_MGP; now also accepts the v7 file (mgp_REL2005_snps_indels.vcf.gz) of Mouse Genomes Project which may be downloaded here: ftp://ftp-mouse.sanger.ac.uk/REL-2004-v7-SNPs_Indels/mgp_REL2005_snps_indels.vcf.gz. INDEL variants are being skipped (this is noted in the report). This new version adds a number of additional strains to choose from, now amounting to 51 strains in total:

Available genomes to choose from are:

SEA_GnJ
SM_J
ST_bJ
CAST_EiJ
BALB_cByJ
NON_LtJ
FVB_NJ
RIIIS_J
CE_J
NZO_HlLtJ
C58_J
BTBR_T+_Itpr3tf_J
MOLF_EiJ
BUB_BnJ
C57L_J
CZECHII_EiJ
C57BL_10J
B10.RIII
AKR_J
C3H_HeJ
LP_J
DBA_2J
QSi3
ZALENDE_EiJ
A_J
PL_J
129S1_SvImJ
NZW_LacJ
PWK_PhJ
C57BL_10SnJ
C57BR_cdJ
QSi5
C57BL_6NJ
SWR_J
MA_MyJ
C3H_HeH
SPRET_EiJ
LEWES_EiJ
WSB_EiJ
129P2_OlaHsd
CBA_J
SJL_J
BALB_cJ
KK_HiJ
JF1_MsJ
NZB_B1NJ
I_LnJ
DBA_1J
129S5SvEvBrd
NOD_ShiLtJ
RF_J

If the file mgp_REL2005_snps_indels.vcf.gz is given, --v7 is set automatically.

• now attempts to extract the fields FORMAT and INFO from the VCF file automatically, to get access to the required information GT (genotype) and FI (filter). See more here.