realign bam

#https://www.biostars.org/p/326714/
java -jar ~/bin/picard.jar SamToFastq I=/mnt/sdb/seqdata/Vacio-luko_dysl/IonCode_0109_rawlib.basecaller.bam FASTQ=0109_filemap.fq
#turetu buti kazkas tokio:
#@RG\tID:Exome1\tLB:Exome1\tSM:Exome1\tPL:ILLUMINA
bwa mem -t 20 -R '@RG\tID:foo\tSM:bar' /mnt/sdb/references/b37/human_g1k_v37.fasta.gz 0109_filemap.fq > 0109.sam
samtools sort 0109.sam > 0109.bam
samtools index 0109.bam