#samtools tview /opt/gotcloudExample/bams/HG00254.bam /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa
#Type “g”, then: “20:42900000”
# "q" to quit

# Look at fastq index file
more /opt/gotcloudExample/GBR2fastq.index

# Look at an input fastq file
# Sequencing data provided to you
less /opt/gotcloudExample/fastq/HG00096_SRR062634_1.fastq
less /opt/gotcloudExample/fastq/HG00096_SRR062634_2.fastq
less /opt/gotcloudExample/fastq/HG00096_SRR062634.fastq

#--------------------------
# Run alignment pipeline
gotcloud align --conf /opt/gotcloudExample/GBR2align.conf --outdir ~/gotcloudTutorial
#--------------------------

# List resulting Output files
ls ~/gotcloudTutorial/bams/*bam
ls ~/gotcloudTutorial/QCFiles/*qplot*
ls ~/gotcloudTutorial/QCFiles/*genoCheck*

# Look at one of the bams using tview
samtools tview ~/gotcloudTutorial/bams/HG00096.recal.bam /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa
# Type "g", then: "20:42900000"
# "q" to quit

# Look at contamination Results
more ~/gotcloudTutorial/QCFiles/*.selfSM

# Look at statistics
more ~/gotcloudTutorial/QCFiles/*.stats

# Look at pdf
okular ~/gotcloudTutorial/QCFiles/HG00096.qplot.pdf


### Variant Calling
# Look at BAM index
more /opt/gotcloudExample/GBR60bam.index

# Look at configuration
more /opt/gotcloudExample/GBR60vc.conf

#--------------------------
# Run snp calling pipeline
gotcloud snpcall --conf /opt/gotcloudExample/GBR60vc.conf --outdir ~/gotcloudTutorial --numjobs 2 --region 20:42900000-43200000
#--------------------------

ls ~/gotcloudTutorial/split/chr20/chr20.filtered*
ls ~/gotcloudTutorial/vcfs/chr20/chr20.filtered*


#--------------------------
# Run ld refinement pipeline
gotcloud ldrefine --conf /opt/gotcloudExample/GBR60vc.conf --outdir ~/gotcloudTutorial --numjobs 2

#--------------------------
ls ~/gotcloudTutorial/thunder/chr20/GBR/thunder/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz