ANGSD

ANGSD is a popgen software for NGS data. Most methods take genotype uncertainty into account instead of basing on called genotypes.

• The software documentation website.
• Tim's usage example.
• Arun's ANGSD-wrapper.

Inbreeding Coefficients Calculations

Method for calculating inbreeding coefficients using ngsF with ANGSD genotype likelihood. See Vieira et al., 2013 for full details on the method.

In this example, we will estimate inbreeding coefficients per individual and incorporate them into the calculation of posterior probabilities. First, calculate genotype likelihoods and call SNPs:

"${ANGSD_DIR}"/angsd \
            -bam "${SAMPLE_LIST}" \
            -r "${REGIONS}" \
            -doGLF "${DO_GLF}" \
            -GL "${GT_LIKELIHOOD}" \
            -out "${OUT}"/"${PROJECT}" \
            -ref "${REF_SEQ}" \
            -anc "${ANC_SEQ}" \
            -doMaf "${DO_MAF}" \
            -SNP_pval "${SNP_PVAL}" \
            -doMajorMinor "${DO_MAJORMINOR}" \
            -minMapQ "${MIN_MAPQ}" \
            -minQ "${MIN_BASEQUAL}" \
            -nThreads "${N_CORES}"

Or glf.gz file to call SNPs.

$ANGSD/angsd -glf $SIM_DATA/testF.glf.gz -fai $SIM_DATA/testAF.ANC.fai -nInd 20 -doGlf 3 -doMajorMinor 1 -doMaf 1 -SNP_pval 1e-4 -out testF.HWE

And then, estimate inbreeding coefficients.

N_SITES=$((`zcat testF.HWE.mafs.gz | wc -l`-1))
zcat testF.HWE.glf.gz | ../ngsF --n_ind 20 --n_sites $N_SITES --glf - --min_epsilon 0.001 --out testF.approx_indF --approx_EM --seed 12345 --init_values r
zcat testF.HWE.glf.gz | ../ngsF --n_ind 20 --n_sites $N_SITES --glf - --min_epsilon 0.001 --out testF.indF --init_values testF.approx_indF.pars

Site Frequency Spectrum (SFS)

#!/usr/bin/env bash

set -e
set -o pipefail

#   Load variables from supplied config file
source "$1"

#   Are we using Common_Config? If so, source it
if [[ -f "${COMMON}" ]]
then
    source "${COMMON}"
fi

#   Where is angsd-wrapper located?
SOURCE=$2

#   Where is ANGSD?
ANGSD_DIR=${SOURCE}/dependencies/angsd

#   Variables created from transforming other variables
#       The number of individuals in the taxon we are analyzing
N_IND=$(wc -l < "${SAMPLE_LIST}")
#       How many inbreeding coefficients are supplied?
N_F=$(wc -l < "${SAMPLE_INBREEDING}")
#       For ANGSD, the actual sample size is twice the number of individuals, since each individual has two chromosomes.
#       The individual inbreeding coefficents take care of the mismatch between these two numbers

#   Perform a check to see if number of individuals matches number of inbreeding coefficients
if [ "${N_IND}" -ne "${N_F}" ]
then
    echo "Mismatch between number of samples in ${SAMPLE_LIST} and ${SAMPLE_INBREEDING}"
    exit 1
fi

#   Create outdirectory
OUT="${SCRATCH}"/"${PROJECT}"/SFS
mkdir -p "${OUT}"

#   Now we actually run the command, this creates a binary file that contains the prior SFS
if [[ -f "${OUT}"/"${PROJECT}"_SFSOut.mafs.gz ]] && [ "$OVERRIDE" = "false" ]
then
    echo "maf already exists and OVERRIDE=false, skipping angsd -bam..."
else
    #   Do we have a regions file?
    if [[ -f "${REGIONS}" ]]
    then
        "${ANGSD_DIR}"/angsd \
            -bam "${SAMPLE_LIST}" \
            -out "${OUT}"/"${PROJECT}"_SFSOut \
            -indF "${SAMPLE_INBREEDING}" \
            -doSaf "${DO_SAF}" \
            -uniqueOnly "${UNIQUE_ONLY}" \
            -anc "${ANC_SEQ}" \
            -minMapQ "${MIN_MAPQ}" \
            -minQ "${MIN_BASEQUAL}" \
            -nInd "${N_IND}" \
            -minInd "${MIN_IND}"\
            -baq "${BAQ}" \
            -ref "${REF_SEQ}" \
            -GL "${GT_LIKELIHOOD}" \
            -P "${N_CORES}" \
            -doMajorMinor "${DO_MAJORMINOR}" \
            -doMaf "${DO_MAF}" \
            -doGeno "${DO_GENO}" \
            -rf "${REGIONS}" \
            -doPost "${DO_POST}"
    #   Are we missing a definiton for regions?
    elif [[ -z "${REGIONS}" ]]
    then
        "${ANGSD_DIR}"/angsd \
            -bam "${SAMPLE_LIST}" \
            -out "${OUT}"/"${PROJECT}"_SFSOut \
            -indF "${SAMPLE_INBREEDING}" \
            -doSaf "${DO_SAF}" \
            -uniqueOnly "${UNIQUE_ONLY}" \
            -anc "${ANC_SEQ}" \
            -minMapQ "${MIN_MAPQ}" \
            -minQ "${MIN_BASEQUAL}" \
            -nInd "${N_IND}" \
            -minInd "${MIN_IND}"\
            -baq "${BAQ}" \
            -ref "${REF_SEQ}" \
            -GL "${GT_LIKELIHOOD}" \
            -P "${N_CORES}" \
            -doMajorMinor "${DO_MAJORMINOR}" \
            -doMaf "${DO_MAF}" \
            -doGeno "${DO_GENO}" \
            -doPost "${DO_POST}"
    #   Assuming a single reigon was defined in config file
    else
        "${ANGSD_DIR}"/angsd \
            -bam "${SAMPLE_LIST}" \
            -out "${OUT}"/"${PROJECT}"_SFSOut \
            -indF "${SAMPLE_INBREEDING}" \
            -doSaf "${DO_SAF}" \
            -uniqueOnly "${UNIQUE_ONLY}" \
            -anc "${ANC_SEQ}" \
            -minMapQ "${MIN_MAPQ}" \
            -minQ "${MIN_BASEQUAL}" \
            -nInd "${N_IND}" \
            -minInd "${MIN_IND}" \
            -baq "${BAQ}" \
            -ref "${REF_SEQ}" \
            -GL "${GT_LIKELIHOOD}" \
            -P "${N_CORES}" \
            -doMajorMinor "${DO_MAJORMINOR}" \
            -doMaf "${DO_MAF}" \
            -doGeno "${DO_GENO}" \
            -doPost "${DO_POST}" \
            -r "${REGIONS}"
    fi
fi

"${ANGSD_DIR}"/misc/realSFS \
    "${OUT}"/"${PROJECT}"_SFSOut.saf.idx \
    -P "${N_CORES}" \
    > "${OUT}"/"${PROJECT}"_DerivedSFS.graph.me

Thetas Estimations