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a guest Jun 19th, 2019 79 Never
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  1. samtools depth -a in1.bam > depth_in1_both.tsv
  2.      
  3. samtools view -b -F 0x10 in1.bam | samtools depth -a > depth_in1_fwd.tsv
  4. samtools view -b -f 0x10 in1.bam | samtools depth -a > depth_in1_rev.tsv
  5.      
  6. bedtools intersect -a in1.bam -b regions.bed |
  7.   samtools view -b -F 0x10 in1.bam |
  8.   samtools depth -a > depth_in1_regions_fwd.tsv
  9.      
  10. paste <(samtools depth -aa in1.bam)
  11.       <(samtools view -b -F 0x10 in1.bam | samtools depth -aa)
  12.       <(samtools view -b -f 0x10 in1.bam | samtools depth -aa) |
  13.   cut -f 1,2,3,6,9 > depth_in1_bfr.tsv
  14.      
  15. paste depth_in1_both.tsv depth_in1_fwd.tsv depth_in1_rev.tsv |
  16.   cut -f 1,2,3,6,9 > depth_in1_bfr.tsv
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