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The final BAM files produced by the mapping pipeline can be found in the files:
The final BAM files produced by the mapping pipeline are:
ls mappingResults/alignment.recal/*.recal.bam
ls mappingResults/alignment.recal/*.recal.bam
Index files (.bai) for these BAMs are also in that directory.
Index files (.bai) for these BAMs are also in that directory.
The QC files for verifyBamID are:
The QC files for verifyBamID are:
[[Understanding QPLOT output]]
[[Understanding QPLOT output]]
==Generating Variant Calls==
The next step is to analyze BAM files by calling SNPs and generating a VCF file containing the results.
The variant calling pipeline has multiple built-in steps to generate BAMs:
# Filter out reads with low mapping quality
# Per Base Alignment Quality Adjustment (BAQ)
# Resolve overlapping paired end reads
# Generate genotype likelihood files
# Perform variant calling
# Extract features from variant sites
# Perform variant filtering
This processing results in a single set of variant sites for all samples.
Run the variant calling pipeline:
umake.pl --conf [[GBR60vc.conf]] --outdir vcResults --snpcall --numjobs 2
TBD - maybe merge both mapping & umake into a single script and have them as options.
TBD - add link explaining the contents of the .conf & .index files.
Upon successful completion of the variant calling pipeline, you will see the following message:
TBD
The final VCF produced by the variant calling pipeline containing only the variants that passed all filters is:
ls vcResults/split/chr20/chr20.filtered.PASS.vcf.gz
The VCF including the filtered sites with the filters marked in the Filter field (or "PASS" if the site was not filtered) is:
ls vcResults/vcf/chr20/chr20.filtered.vcf.gz
TBD what sort of post analysis is necessary???
==Linkage Disequilibrium-Aware Geontype Refinement==
Instructions for running Beagle/Thunder.
Maybe these should be built into
= Modifying the Tutorial Inputs to Run Your Own Data =
== Mapping Pipeline ==
The inputs to the mapping pipeline are
===Index file===
===Index file===
