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cellBasisVector1 108.8612 0.0 0.0

cellBasisVector2 0.0 108.8612 0.0

cellBasisVector3 0.0 0.0 77.758

cellOrigin 0.0 0.0 0.0

coordinates apoa1.pdb

temperature 300

seed 74269

switching on

switchdist 10

cutoff 12

pairlistdist 13.5

margin 0

stepspercycle 20

PME on

PMEGridSizeX 108

PMEGridSizeY 108

PMEGridSizeZ 80

structure apoa1.psf

parameters par_all22_prot_lipid.xplor

parameters par_all22_popc.xplor

exclude scaled1-4

1-4scaling 1.0

timestep 1.0

fullElectFrequency 4

numsteps 500

outputtiming 100

outputEnergies 100

outputname [output file]

Step 2. GenotypeGVCFs

java -d64 -Xms8g -Xmx30g -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -nt [number of threads] -R [reference chromosome] -V

[gvcf output] -o [raw vcf]

Phase 3. Preliminary analyses

Step 1. Variant recalibration

java -d64 -Xms512m -Xmx2g -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R [reference chromosome] --input [raw vcf] -an

QD -an DP -an FS -an ReadPosRankSum -U LENIENT_VCF_PROCESSING --mode SNP --recal_file [raw vcf recalibration] --

tranches_file [raw vcf tranches]

Step 2. Apply recalibration

java -d64 -Xms512m -Xmx2g -jar GenomeAnalysisTK.jar -T ApplyRecalibration -R [reference chromosome] -input [raw vcf] -o

[recalibrated filtered vcf] --ts_filter_level 99.97 --tranches_file [raw vcf tranches] --recal_file [raw vcf recalibration] --mode SNP -U

LENIENT_VCF_PROCESSING

NAMD commands

namd2 +p [number of threads] [run configuration file]

Example of a configuration file