on bitwise flag values sam_bitwise_flag_filter.py --input_sam_file=$input1 --flag_column=2 #for $bit in $bits '${bit.flags}=${bit.states}' #end for > $out_file1 Read is paired Read is mapped in a proper pair The read is unmapped The mate is unmapped Read strand Mate strand Read is the first in a pair Read is the second in a pair The alignment or this read is not primary The read fails platform/vendor quality checks The read is a PCR or optical duplicate No Yes

**What it does** Allows parsing of SAM datasets using bitwise flag (the second column). The bits in the flag are defined as follows:: Bit Info ------ -------------------------------------------------------------------------- 0x0001 the read is paired in sequencing, no matter whether it is mapped in a pair 0x0002 the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment) 1 0x0004 the query sequence itself is unmapped 0x0008 the mate is unmapped 1 0x0010 strand of the query (0 for forward; 1 for reverse strand) 0x0020 strand of the mate 1 0x0040 the read is the first read in a pair (see below) 0x0080 the read is the second read in a pair (see below) 0x0100 the alignment is not primary (a read having split hits may have multiple primary alignment records) 0x0200 the read fails platform/vendor quality checks 0x0400 the read is either a PCR duplicate or an optical duplicate Note the following: - Flag 0x02, 0x08, 0x20, 0x40 and 0x80 are only meaningful when flag 0x01 is present. - If in a read pair the information on which read is the first in the pair is lost in the upstream analysis, flag 0x01 should be set, while 0x40 and 0x80 should both be zero. ----- **Example** Suppose the following dataset was generated with BWA mapper:: r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTA * r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA * r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1 r004 0 ref 16 30 6M14N5M * 0 0 ATAGCTTCAGC * r003 16 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0 r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT * To select properly mapped pairs, click the **Add new Flag** button and set *Read mapped in a proper pair* to **Yes**. The following two reads will be returned:: r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTA * r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT * For more information, please consult the `SAM format description`__. .. __: http://www.ncbi.nlm.nih.gov/pubmed/19505943