Post date: Aug 30, 2015 5:50:24 PM
All 384 sam alignments were compressed, sorted and indexed with samtools, using wrap_qsub_rc_sam2bam.pl.
Here is an example for one alignment file:
cd /labs/evolution/data/timema/sperm/Alignments/
samtools view -b -S -o /labs/evolution/data/timema/sperm/Alignments/aln_195105_712517.bam /labs/evolution/data/timema/sperm/Alignments/aln_195105_712517.sam
rm /labs/evolution/data/timema/sperm/Alignments/aln_195105_712517.sam
samtools sort /labs/evolution/data/timema/sperm/Alignments/aln_195105_712517.bam /labs/evolution/data/timema/sperm/Alignments/aln_195105_712517.sorted
rm /labs/evolution/data/timema/sperm/Alignments/aln_195105_712517.bam
samtools index /labs/evolution/data/timema/sperm/Alignments/aln_195105_712517.sorted.bam
PCR duplicates were then removed with samtools and the bam files were re-indexed using wrap_qsub_rc_rmdup.pl.
Here is an example:
cd /labs/evolution/data/timema/sperm/Alignments/
samtools rmdup /labs/evolution/data/timema/sperm/Alignments/aln_195105_712517.sorted.bam /labs/evolution/data/timema/sperm/Alignments/aln_195105_712517_unique.bam
samtools index /labs/evolution/data/timema/sperm/Alignments/aln_195105_712517_unique.bam
rm /labs/evolution/data/timema/sperm/Alignments/aln_195105_712517.sorted.bam