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= BAM File Recovery =
= BAM File Recovery =
A BAM file that has been corrupted, or truncated due to a copy or disk problem can often be partially recovered.
A BAM file that has been corrupted or truncated due to a copy or disk problem can often be partially recovered.
Both the BGZF format and binary BAM format have enough information to scan forward and resynchronize the input data. While some data will be lost, substantial recovery can often be done.
Both the BGZF format and binary BAM format have enough information to scan forward and resynchronize the input data. While some data will be lost, substantial recovery can often be done.
Currently, no statistics are printed as far as how many BAM records are recovered, but subsequent tests can readily be done on the resulting file to determine the quality of recovery.
Currently, no statistics are printed as far as how many BAM records are recovered, but subsequent tests can readily be done on the resulting file to determine the quality of recovery.
In real cases, we have recovered better than 94% of reads from a set of severely damaged files (numerous 64K chunks of a RAID were lost), and better than 99.9% recovery from a moderately damaged file (3 disk pages were corrupt).
= Usage =
= Usage =
