bedtools samtools samtools bedtools '$out_file1' && echo "Moo" >> '$out_file1' && samtools >> '$out_file1' 2>&1 && echo "Cow" >> '$out_file1' && touch "\${TMP:-/tmp}/job_tmp" && touch "\${TEMP:-/tmp}/job_temp" && touch "\${TMPDIR:-/tmp}/job_tmpdir" ]]> 10.1093/bioinformatics/btq033 @misc{SAM_def, title={Definition of SAM/BAM format}, url = {https://samtools.github.io/hts-specs/},} 10.1093/bioinformatics/btp352 10.1093/bioinformatics/btr076 10.1093/bioinformatics/btr509 @misc{Danecek_et_al, Author={Danecek, P., Schiffels, S., Durbin, R.}, title={Multiallelic calling model in bcftools (-m)}, url = {http://samtools.github.io/bcftools/call-m.pdf},} @misc{Durbin_VCQC, Author={Durbin, R.}, title={Segregation based metric for variant call QC}, url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} @misc{Li_SamMath, Author={Li, H.}, title={Mathematical Notes on SAMtools Algorithms}, url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} @misc{SamTools_github, title={SAMTools GitHub page}, url = {https://github.com/samtools/samtools},}