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DeepVariantTrainedSNPCalling
DeepVariantTrainedSNPCalling
 
 
DeepVariantTrainedSNPCalling_0.10.0
DeepVariantTrainedSNPCalling_0.10.0
 
 
DeepVariantTraining
DeepVariantTraining
 
 
MendelianErrors
MendelianErrors
 
 
SNP-sets
SNP-sets
 
 
deepvariant
deepvariant
 
 
dv-first-round-run/vcfs
dv-first-round-run/vcfs
 
 
sambamba
sambamba
 
 
src
src
 
 
README
README
 
 
README.md
README.md
 
 
additional_processing.sh
additional_processing.sh
 
 
assess_variant_calls.nf
assess_variant_calls.nf
 
 
combine.nf
combine.nf
 
 
deepvariant.bash
deepvariant.bash
 
 
deepvariant.nf
deepvariant.nf
 
 
dv-vcf-merge.sh
dv-vcf-merge.sh
 
 
dv_call_variants.bash
dv_call_variants.bash
 
 
dv_call_variants_help.bash
dv_call_variants_help.bash
 
 
dv_help.bash
dv_help.bash
 
 
dv_make_examples.bash
dv_make_examples.bash
 
 
dv_postprocess.bash
dv_postprocess.bash
 
 
dv_run.bash
dv_run.bash
 
 
dv_run_previous.bash
dv_run_previous.bash
 
 
fb-vcf-concat.sh
fb-vcf-concat.sh
 
 
find_missing.pl
find_missing.pl
 
 
find_missing_round2.pl
find_missing_round2.pl
 
 
find_missing_round3.pl
find_missing_round3.pl
 
 
formatted_bird_list_manual.csv
formatted_bird_list_manual.csv
 
 
freebayes.missing.nf
freebayes.missing.nf
 
 
freebayes.missing2.nf
freebayes.missing2.nf
 
 
freebayes.missing4.nf
freebayes.missing4.nf
 
 
freebayes.nf
freebayes.nf
 
 
freebayes.postprocessing.nf
freebayes.postprocessing.nf
 
 
nextflow.config
nextflow.config
 
 
prepare_for_SNP_calling.sh
prepare_for_SNP_calling.sh
 
 
test.nf
test.nf
 
 

README.md

prepare.sh

Copy CRAM files (and indices) over so we can combined them. Also delete Sarah-2 due to poor read alignment (sequencing error).

combine.nf

Combine all reads for a sample into a single CRAM file, example: Sarah_001, Sarah_002, Sarah_003, etc... go into Sarah.cram

alignments/

This leaves combined samples in alignments/ (with indices)

Run FreeBayes

FreeBayes crashed in regions of high-depth due to cluster configuration. To re-run the missing ones, see the freebayes.missing.* files. Please note accuracy of FreeBayes was so low based off of pedigree inheritance (Mendelian inheritance errors) that is was quickly dropped from future analyses.

DeepVariant

See directories: deepvariant/, DeepVariantTraining/, and DeepVariantTraingSNPCalling/.

If you wish to do your own training for DeepVariant, I am developing a more general-purpose NextFlow pipeline that is more clear and uses the newest version. Please be in touch.