A nextflow pipeline for the basic post-processing of human shotgun or capture libraries (not metagenomics samples). See the overview below for the workflow.
The pipeline runs with
- Nextflow v22.10 or larger
- Singularity or Docker
Note: To run nextflow+singularity, your kernel needs to support user-namespaces (see here or here). NOTE: The pipeline is configured to work within the computational environment of the Max-Planck-Institute for Evolutionary Anthropology.
Do not use version v0.5, as it contains a critical bug! Use version v0.6 or later!
NXF_VER=24.04.4
nextflow run mpieva/postprocessing -r v0.12 --split SPLIT -profile PROFILE [OPTIONS]
use the -r v0.12 flag to run a specific version of the pipeline
The pipeline starts with a directory of already demultiplexed and mapped BAM-files, provided with the --split flag. Unmapped and unmerged paired sequences are removed in the analyzeBAM step.
--help Display the HELP Text
--split PATH [required] A directory with demultiplexed and mapped BAM-files
(mapped to the genome specified in --reference_file)
--reference_file FASTA [required] Reference genome used for mapping, required for 'samtools calmd'
--reference_name NAME [required] The folder/name of the reference in '/mnt/solexa/Genomes/' (e.g. hg19_evan).
Used for naming output files and for double-checking the bam-header
--target_file BED [optional] Targetfile (BED) for subsetting BAM to 'ontarget' sequences
--target_name NAME [optional] Name of the target for naming output-files (default: shotgun)
--bamfilter_minlength N [optional] Minimum length of retained sequences (default: 35)
--bamfilter_minqual N [optional] Minimum mapping quality of retained sequences (default: 25)
--bamfilter_keep_vendorfail [optional] Keep reads in bamfile that have the "vendor failed" flag
--deduplication_tool NAME [required] select deduplication tool (default: dedupBAM)
[bam-rmdup, dedupBAM]
--bamrmdup_cheap [optional] Bam-rmdup 'cheap' computation: skip the consensus calling
--bamrmdup_circular CHR:LEN [optional] Bam-rmdup 'circular' option - CHR is circular with length LEN
Profiles can be set with the -profile flag (only one dash!!). They preserve parameters (target-file and references) for different common analyses.
The follwing profiles are available
shotgun {
reference_file = "/mnt/solexa/Genomes/hg19_evan/whole_genome.fa"
reference_name = "hg19_evan"
target_name = "shotgun"
target_file = false
}
AA108_AA115_archaicAdmixture {
// Reference: Fu et al, 2015 (An early modern human from Romania with a recent Neanderthal ancestor), Panel 4
reference_file = "/mnt/solexa/Genomes/hg19_evan/whole_genome.fa"
reference_name = "hg19_evan"
target_name = "AA108_AA115_archaicAdmixture"
target_file = "/home/public/AncientDNA/probe_designs/AA108-115_archaic_admixture/Archaic.align.noN.sorted.bed"
}
AA288_AA292_archaicPlus {
// Reference: TBD
reference_file = "/mnt/solexa/Genomes/hg19_evan/whole_genome.fa"
reference_name = "hg19_evan"
target_name = "AA288_AA292_archaicPlus"
target_file = "/home/public/AncientDNA/probe_designs/AA288-AA292_ArchaicPlus_WORKING_AltRef/ArchaicPlus_v3_final_TRF_sorted.bed"
}
AA293_AA295_archaicPlus_thirdAllele_hg19 {
// Reference: TBD
reference_file = "/mnt/solexa/Genomes/hg19_evan/whole_genome.fa"
reference_name = "hg19_evan"
target_name = "AA293_AA295_archaicPlus_thirdAllele"
target_file = "/home/public/AncientDNA/probe_designs/AA293-AA295_ArchaicPlus_WORKING_thirdAllele/ ArchaicPlus_v3_final_TRF_sorted_52bp_ALT_REF_THIRD.bed"
}
AA293_AA295_archaicPlus_thirdAllele_hg19_3rd {
// Reference: TBD
reference_file = "/mnt/solexa/Genomes/hg19_evan_3rdBaseRef_withY/whole_genome.fa"
reference_name = "hg19_evan_3rdBaseRef_withY"
target_name = "AA293_AA295_archaicPlus_thirdAllele"
target_file = "/home/public/AncientDNA/probe_designs/AA293-AA295_ArchaicPlus_WORKING_thirdAllele/ ArchaicPlus_v3_final_TRF_sorted_52bp_ALT_REF_THIRD.bed"
}
AA293_AA295_archaicPlus_thirdAllele_hg19_alt {
// Reference: TBD
reference_file = "/mnt/solexa/Genomes/hg19_evan_ArchaicRef_withY/whole_genome.fa"
reference_name = "hg19_evan_ArchaicRef_withY"
target_name = "AA293_AA295_archaicPlus_thirdAllele"
target_file = "/home/public/AncientDNA/probe_designs/AA293-AA295_ArchaicPlus_WORKING_thirdAllele/ ArchaicPlus_v3_final_TRF_sorted_52bp_ALT_REF_THIRD.bed"
}
AA213_1240k {
// Reference: Fu et al, 2015 (An early modern human from Romania with a recent Neanderthal ancestor), Panel 1+2
reference_file = "/mnt/solexa/Genomes/hg19_evan/whole_genome.fa"
reference_name = "hg19_evan"
target_name = "AA213_1240k"
target_file = "/mnt/archgen/Reference_Genomes/Human/hs37d5/SNPCapBEDs/1240K.pos.list_hs37d5.0based.bed"
}
Twist_1240k {
// Reference: Roland et al, 2022 (Three assays for in-solution enrichment of ancient human DNA at more than a million SNP)
reference_file = "/mnt/solexa/Genomes/hg19_evan/whole_genome.fa"
reference_name = "hg19_evan"
target_name = "Twist_1240k"
target_file = "/home/public/AncientDNA/probe_designs/TW1_Reich_Panel/gs01.target_positions_hg19.bed"
}
AA163_humanMT {
// Reference: ?
bamrmdup_circular '"gi|251831106|ref|NC_012920.1|":16565'
reference_file = "/mnt/solexa/Genomes/human_MT/whole_genome.fa"
reference_name = "human_MT"
target_name = "AA163"
}
# ELEPHANT
shotgun_loxAfr4 {
reference_file = "/mnt/solexa/Genomes/loxAfr4/whole_genome.fa"
reference_name = "loxAfr4"
target_name = "shotgun"
target_file = false
}
shotgun_ratNor6{
reference_file = "/mnt/solexa/Genomes/ratNor6/whole_genome.fa"
reference_name = "ratNor6"
target_name = "shotgun"
target_file = false
}
shotgun_varKom{
reference_file = "/mnt/solexa/Genomes/varKom/whole_genome.fa"
reference_name = "varKom"
target_name = "shotgun"
target_file = false
}
