bam and sam commands e.g. Convert Bam to Sam, sam to fastq

convert bam to sam:  $ samtools view -h -o out.sam in.bam

convert sam to bam:  $ samtools view -bT .faFILE samfile

sort the bam:  $ samtools sort Example.bam Example.sorted

view a specific region(must be properly indexed while indexing depends on sorting):

$ samtools view Example.bam chr17:220-300

Print the header of bam

samtools view -H in.bam


The end of sam file has the bowtie parameters used.


sam to fastq

cat samplename.nomapping.sam | grep -v ^@ | awk '{print "@"$1"\n"$10"\n+\n"$11}' > unmapped/samplename.fastq