##general header## This ftp site provides access to the genomic resources for wild mouse species generated at the Max-Planck Institute for Evolutionary Biology in Plšn ( http://www.evolbio.mpg.de/ ), Department of Evolutionary Genetics (Diethard Tautz). The details are published in: Harr et al. Genomic resources for wild populations of the house mouse, Mus musculus, and its close relative Mus spretus. Scientific data (2016). ##specific information for directory /vcf ## This directory includes two cumulative vcf files based on the joint vcf calling across all populations, sub-species and species in the study. The file includes all identified SNPs and indels. The high quality SNPs (90% VQSR tranche) are labelled "PASS" in the "VQSR FLAG" column. The file is reduced to filltered (PASS) SNPs and MNPs. The sub-directory /vcf/GVCF includes all GVCF files for all individuals. ##specific information for directory /vcf/pop_vcf ##^M The sub-directory /vcf/pop_vcf contains population specific vcf files filtered to only contain high quality SNPs and 'Multi-NucleotidePolymorphisms' MNPs (see https://software.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_annotator_VariantType.php) labelled as "PASS" (90% VQSR tranche). In addition all unused alternate alleles were removed from each population as well as non variant sites as compared to the reference for each population. All population specific files were generated with the following GATK command using as the input VCF file: #java -jar GenomeAnalysisTK.jar -T SelectVariants -R -V -o $OUTPUT -selectType SNP -selectType MNP \ #--excludeFiltered --excludeNonVariants --removeUnusedAlternates -sn $SAMPLE1 -sn $SAMPLE2 ... List of samples per population: Mmd_FRA: Mmd_FRA1_14.variant,Mmd_FRA2_15B.variant,Mmd_FRA3_16B.variant,Mmd_FRA4_18B.variant,Mmd_FRA5_B2C.variant,Mmd_FRA6_C1.variant,Mmd_FRA7_E1.variant,Mmd_FRA8_F1B.variant Mmd_GER: Mmd_GER1_TP1.variant2,Mmd_GER2_TP121B.variant2,Mmd_GER3_TP17-2.variant2,Mmd_GER4_TP3-92.variant2,Mmd_GER5_TP4a.variant2,Mmd_GER6_TP51D.variant2,Mmd_GER7_TP7-10F1A2.variant2,Mmd_GER8_TP81B.variant2 Mmd_IRA: Mmd_IRA1_AH15.variant3,Mmd_IRA2_AH23.variant3,Mmd_IRA3_JR11.variant3,Mmd_IRA4_JR15.variant3,Mmd_IRA5_JR2-F1C.variant3,Mmd_IRA6_JR5-F1C.variant3,Mmd_IRA7_JR7-F1C.variant3,Mmd_IRA8_JR8-F1A.variant3 Mmd_HEL: Mmd_HEL1_HG06.variant4,Mmd_HEL2_HG08.variant4,Mmd_HEL3_HG13.variant4 Mmm_CZE: Mmm_CZE1_CR12.variant5,Mmm_CZE2_CR13.variant5,Mmm_CZE3_CR16.variant5,Mmm_CZE4_CR23.variant5,Mmm_CZE5_CR25.variant5,Mmm_CZE6_CR29.variant5,Mmm_CZE7_CR46.variant5,Mmm_CZE8_CR59.variant5 Mmm_KAZ: Mmm_KAZ1_AL1.variant6,Mmm_KAZ2_AL16.variant6,Mmm_KAZ3_AL19.variant6,Mmm_KAZ4_AL33.variant6,Mmm_KAZ5_AL38.variant6,Mmm_KAZ6_AL40.variant6,Mmm_KAZ7_AL41.variant6,Mmm_KAZ8_AL42.variant6 Mmm_AFG: Mmm_AFG1_396.variant7,Mmm_AFG2_413.variant7,Mmm_AFG3_416.variant7,Mmm_AFG4_424.variant7,Mmm_AFG5_435.variant7,Mmm_AFG6_444.variant7 Mmc_CAST: Mmc_CAST10_H36.variant8,Mmc_CAST1_H12.variant8,Mmc_CAST2_H14.variant8,Mmc_CAST3_H15.variant8,Mmc_CAST4_H24.variant8,Mmc_CAST5_H26.variant8,Mmc_CAST6_H27.variant8,Mmc_CAST7_H28.variant8,Mmc_CAST8_H30.variant8,Mmc_CAST9_H34.variant8 Ms_SPRE: Ms_SPRE1_SP36.variant9,Ms_SPRE2_SP39.variant9,Ms_SPRE3_SP41.variant9,Ms_SPRE4_SP51.variant9,Ms_SPRE5_SP62.variant9,Ms_SPRE6_SP68.variant9,Ms_SPRE7_SP69.variant9,Ms_SPRE8_SP70.variant9