#! /bin/bash
RMD="/path/to/script/remove_duplicate_by_pos.py" #e.g. /data/tanoramb/Scripts/v2/remove_duplicate_by_pos.py in Astro
TABIX="/path/to/software/Tabix/tabix-0.2.6/tabix"
PARALLEL="/path/to/script/parallel.sh" #e.g. /data/tanoramb/Scripts/other/parallel.sh in Astro 

NCPU=10 #Number of CPUs

# VCF files are named as "1KG_PEL_chr*.recode.vcf" where "*" is the number of the chromosome 1 through 22
# Then the VCF files are processed to remove duplicated positions, bgzipped, and indexed.
${PARALLEL} -j ${NCPU} -r "${RMD} -i 1KG_PEL_chr*.recode.vcf -o 1KG_PEL_chr*.recode.rmd.vcf > rmd.chr*.log 2>&1" $(seq 1 22)
${PARALLEL} -j ${NCPU} -r "bgzip 1KG_PEL_chr*.recode.rmd.vcf" $(seq 1 22)
${PARALLEL} -j ${NCPU} -r "${TABIX} -p vcf 1KG_PEL_chr*.recode.rmd.vcf.gz" $(seq 1 22)

BCFTOOLS="/path/to/software/BCFTools/bcftools-1.10.2/bcftools"

IDS90="ids_pel_ge90.txt" #Text file containing Sample IDs to keep from VCF file. In this case, those Samples with more than 90% Native-American ancestry (analysis done elsewhere)
IDS95="ids_pel_ge95.txt" #Text file containing Sample IDs to keep from VCF file. In this case, those Samples with more than 95% Native-American ancestry (analysis done elsewhere)

# VCF files are gunzipped
${PARALLEL} -j ${NCPU} -r "gunzip -k 1KG_PEL_chr*.recode.rmd.vcf.gz" $(seq 1 22)

# We run bcftools for both percentages 90% and 95%, and to keep the corresponding samples. Then the files are bgzipped and indexed.
for PCT in 90 95; do
    IDS="ids_pel_ge${PCT}.txt"
    ${PARALLEL} -j ${NCPU} -r "${BCFTOOLS} view -S ${IDS} 1KG_PEL_chr*.recode.rmd.vcf > 1KG_PEL_chr*.recode.rmd.ge${PCT}.vcf" $(seq 1 22)
    ${PARALLEL} -j ${NCPU} -r "bgzip 1KG_PEL_chr*.recode.rmd.ge${PCT}.vcf" $(seq 1 22)
    ${PARALLEL} -j ${NCPU} -r "${TABIX} -p vcf 1KG_PEL_chr*.recode.rmd.ge${PCT}.vcf.gz" $(seq 1 22)
done
\rm -rf .tmp* *.vcf

#! /bin/bash
# Script that calls the master script for all chromosomes in a parallel fashion for each chromosome
  
NCPU=10 #Number of CPUs

PARALLEL="/path/to/script/parallel.sh" #e.g. /data/tanoramb/Scripts/other/parallel.sh in Astro
SCRIPT="/path/to/script/master_script_data_beagle5_rfmix15and20.sh"
#SCRIPT="/path/to/script/master_script_data_shapeit_rfmix20.sh" #If the phasing must be done using ShapeIT and RFMix 2.0 only
${PARALLEL} -j ${NCPU} -r "${SCRIPT} -c=* > data.chr*.log 2>&1" 1 22 2 21 3 20 4 19 5 18 6 17 7 16 8 15  9 14 10 13 11 12

#IF RFMix 2.0 is run later
POPS=("PEL" "IBS" "YRI")
echo "" > refs.sample_map.tsv; :> refs.sample_map.tsv
for POP in ${POPS[*]}; do
    name=$(echo ${POP} | awk '{print tolower($0)}')
    gunzip -c phased.intersected.norm.${name}.chr22.vcf.gz | grep "#CHROM" | cut -f10- | sed 's/\t/\n/g' | awk -v group="${POP}" '{print $1"\t"group}' >> refs.sample_map.tsv
done

#! /bin/bash
  
NCPU=10 #Number of CPUs

PARALLEL="/path/to/script/parallel.sh" #e.g. /data/tanoramb/Scripts/other/parallel.sh in Astro

RFMIX20="/path/to/Software/RFmix/RFMix2/rfmix"  #e.g. /data/tanoramb/Software/RFmix/RFMix2/rfmix in Astro
MAPS="/path/to/Data/recombinationmaps/rfmix" #e.g. /data/tanoramb/Data/recombinationmaps/rfmix in Astro
DIR="/path/to/data" #Path to directory containing files and subdirectories generated by Master script of previous step 

${PARALLEL} -j ${NCPU} -r "${RFMIX20} -f ${DIR}/phased.intersected.norm.chi.chr*.vcf.gz -r ${DIR}/phased.intersected.norm.REFS.chr*.vcf.gz -m ${DIR}/refs.sample_map.tsv -g ${MAPS}/chr*.rfmix.map -o rfmix20.chi.chr*.deconvoluted --chromosome=* > rfmix20.chr*.log 2>&1" 1 22 2 21 3 20 4 19 5 18 6 17 7 16 8 15 9 14 10 13 11 12

#! /bin/bash
  
NCPU=10 #Number of CPUs

PARALLEL="/path/to/script/parallel.sh" #e.g. /data/tanoramb/Scripts/other/parallel.sh in Astro

RFMIX15="/path/to/Software/RFmix/RFMix_v1.5.4/PopPhased/RFMix_PopPhased"  #e.g. /data/tanoramb/Software/RFmix/RFMix_v1.5.4/PopPhased/RFMix_PopPhased in Astro
DIR="/path/to/data/rfmix15_files" #Path to directory containing files for RFMix 1.5 generated by Master script of previous step.

${PARALLEL} -j ${NCPU} -r "${RFMIX15} -a ${DIR}/rfmix15.chr*.rfmix15.hap -p ${DIR}/rfmix15.chr*.rfmix15.class -m ${DIR}/pos_chr*.cm.txt -fb 1 -w 0.2 -o rfmix15.out.chr* > rfmix15.chr*.log 2>&1" 1 22 2 21 3 20 4 19 5 18 6 17 7 16 8 15 9 14 10 13 11 12

#Gzipping heavy files
for CHR in $(seq 1 22); do
    gzip rfmix15.out.chr${CHR}.0.ForwardBackward.txt
    gzip rfmix15.out.chr${CHR}.allelesRephased0.txt
done

#! /bin/bash
  
 
DATA="/path/to/data" #Path to directory containing files and subdirectories generated by Master script in step 2
RFMIX2DIR="/path/to/rfmix2_data" #Path to directory containing files generated by RFMix 2.0 in step 3
UKMSP="python /path/to/Software/Tractor/UnkinkMSPfile.py" #e.g. /data/tanoramb/Software/Tractor/UnkinkMSPfile.py in Astro
UKGEN="python /path/to/Software/Tractor/UnkinkGenofile.py" #e.g. /data/tanoramb/Software/Tractor/UnkinkGenofile.py in Astro

for CHR in $(seq 1 22); do
    cp -s ${RFMIX2DIR}/rfmix20.chi.chr${CHR}.deconvoluted* .
    echo "Unkinking MSP file - CHR ${CHR}"
    ${UKMSP} --msp rfmix20.chi.chr${CHR}.deconvoluted
    echo "Gunzipping VCF CHR ${CHR}"
    gunzip -c ${DATA}/phased.intersected.norm.chi.chr${CHR}.vcf.gz > phased.intersected.norm.chi.chr${CHR}.vcf
    echo "Unkinking VCF CHR ${CHR}"
    ${UKGEN} --switches rfmix20.chi.chr${CHR}.deconvoluted.switches.txt --genofile phased.intersected.norm.chi.chr${CHR}
    echo "DONE CHR ${CHR}"
done

#! /bin/bash
  
DIR="/path/to/rfmix2_data" #Path to directory containing files generated by RFMix 2.0 in step 3

head -n 1 ${DIR}/rfmix20.chi.chr1.deconvoluted.msp.tsv | cut -d":" -f2 | awk '{print $1"\n"$2"\n"$3}' > rfmix20.Viterbi.coding.txt
sed -n 2p ${DIR}/rfmix20.chi.chr1.deconvoluted.msp.tsv | cut -f7- | sed 's/\t/\n/g' > rfmix20.Viterbi.columns.txt

for CHR in $(seq 1 22); do
    tail -n +3 ${DIR}/rfmix20.chi.chr${CHR}.deconvoluted.msp.tsv | cut -f7- | sed 's/\t/ /g' | sed 's/$/ /g' > rfmix20.out.chr${CHR}.0.Viterbi.txt
done