hg002_experiments.sh

#!/bin/bash
export JB2DIR=~/src/jbrowse-components/test_data/hg002
export NCBIROOT=https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son

## download chr22 from the Illumina 2x250bp reads and 300x reads
samtools view $NCBI_ROOT/NIST_Illumina_2x250bps/novoalign_bams/HG002.hs37d5.2x250.bam 22 -o HG002.hs37d5.2x250.chr22.bam
samtools view $NCBI_ROOT/NIST_HiSeq_HG002_Homogeneity-10953946/NHGRI_Illumina300X_AJtrio_novoalign_bams/HG002.hs37d5.300x.bam 22 -o HG002.hs37d5.300x.chr22.bam


## select chr22 out of the HG002 T2T assembly, contains a full chromosome for PATERNAL and MATERNAL
samtools faidx 'https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/scratch/HG002/assemblies/drafts/assembly.v0.7.fasta' chr22_PATERNAL > chr22_PATERNAL.fasta
samtools faidx 'https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/scratch/HG002/assemblies/drafts/assembly.v0.7.fasta' chr22_MATERNAL > chr22_MATERNAL.fasta
wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
gunzip hs37d5.fa.gz
samtools faidx hs37d5.fa
samtools faidx hs37d5.fa 22 > hg19_chr22.fa

## combine
cat chr22_*.fasta > chr22.fa




## convert GIAB bam to FASTQ and then re-align to new combined mat+pat chr22.fa
for COV in 2x250 300x; do
  samtools collate -u -O HG002.hs37d5.$COV.chr22.bam | samtools fastq -1 $COV.paired1.fq -2 $COV.paired2.fq -0 /dev/null -s /dev/null -n
  quickalign_paired.sh chr22.fa $COV.paired1.fq $COV.paired2.fq $COV.cram
done;

## add assemblies to jbrowse 2
for VAR in MATERNAL PATERNAL; do
  ## add assembly to JBrowse 2 (maternal and paternal added as 'separate genome assemblies')
  jbrowse add-assembly chr22_$VAR.fasta --out $JB2DIR --load copy
done;

# add cram tracks and bigwigs
for VAR in MATERNAL PATERNAL; do
  for COV in 2x250 300x; do
    samtools view $COV.cram chr22_$VAR -o "${COV}_${VAR}".cram
    samtools index "${COV}_${VAR}".cram
    jbrowse add-track "${COV}_${VAR}".cram --out $JB2DIR --load copy -a chr22_$VAR --force
    mosdepth "${COV}_${VAR}".cram -b 100 -f chr22.fa "${COV}_${VAR}".cram
    gunzip "${COV}_${VAR}".cram.per-base.bed.gz
    bedGraphToBigWig "${COV}_${VAR}".cram.per-base.bed chr22.fa.fai "${COV}_${VAR}".cram.per-base.bw
    jbrowse add-track "${COV}_${VAR}".cram.per-base.bw --out $JB2DIR --load copy -a chr22_$VAR --force
  done;
done;


## whole-genome alignment of chr22_MATERNAL vs chr22_PATERNAL with and without CIGAR (without a bit faster)
minimap2 -x asm5 chr22_MATERNAL.fasta chr22_PATERNAL.fasta > chr22_MATERNAL_vs_PATERNAL.paf
minimap2 -c -x asm5 chr22_MATERNAL.fasta chr22_PATERNAL.fasta > chr22_MATERNAL_vs_PATERNAL_cigar.paf

## load whole-genome alignment as a 'synteny track' into jbrowse 2
jbrowse add-track chr22_MATERNAL_vs_PATERNAL_cigar.paf -a chr22_PATERNAL,chr22_MATERNAL --out $JB2DIR --load copy