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Local realignment of insertions and deletions is performed using IndelRealigner. Both steps of this process are implemented using GATK. the tumor BAM and normal tissue BAM) associated with the same patient. However, in other cases a sorted BAM file prior to marking duplicates may be desired. Co-cleaning is performed as a separate pipeline as it uses multiple BAM files (i.e. #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 Sample2 Sample3 Sample4 Sample5 GATK’s duplicate marking tools perform more efficiently with queryname-grouped input as generated by the aligner and produce sorted BAM output so the most efficient pipeline would not write sorted BAM files from the aligner. Adding header information to the BAM files. Some support the CRAM format, but we have observed performance issues when working directly from CRAM files, so in our own work we convert CRAM to BAM first, and we only use CRAM for archival purposes. #reference=file:///home/msk8/data/PTC_Human.fa All GATK tools that take in mapped read data expect a BAM file as primary format.