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ionox0/Bam_Compare

Created October 5, 2018 18:22
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Indel Realignment comparison
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Bam_Compare
# Compare first 11 fields of bam files
diff <(samtools view 5500-FC-FGFR2-spike-in/Sample_ML-fgfr2-015-pl-T02_/ML-fgfr2-015-pl-T02_IGO_05500_FC_16_S16_001_cl_aln_srt_MD_IR_FX_BR.bam | cut -f1-11 ) <(samtools view repeat-run/5500-FC-FGFR2-spike-in/Sample_ML-fgfr2-015-pl-T02_/ML-fgfr2-015-pl-T02_IGO_05500_FC_16_S16_001_cl_aln_srt_MD_IR_FX_BR.bam | cut -f1-11 ) > ~/ML-fgfr2-015-pl-T02_IGO_05500_FC_16_S16_001_cl_aln_srt_MD_IR_FX_BR-complete_diff-original_vs_repeat-run
# Compare IR reads (grep for "YO:" tag)
diff <(samtools view 5500-FC-FGFR2-spike-in/Sample_ML-fgfr2-015-pl-T02_/ML-fgfr2-015-pl-T02_IGO_05500_FC_16_S16_001_cl_aln_srt_MD_IR_FX_BR.bam | grep "YO:") <(samtools view repeat-run/5500-FC-FGFR2-spike-in/Sample_ML-fgfr2-015-pl-T02_/ML-fgfr2-015-pl-T02_IGO_05500_FC_16_S16_001_cl_aln_srt_MD_IR_FX_BR.bam | grep "YO:") > ~/ML-fgfr2-015-pl-T02_IGO_05500_FC_16_S16_001_cl_aln_srt_MD_IR_FX_BR-indel_realign_diff-original_vs_repeat-run
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