Hello
I want to align my reads to the reference genome and then use GATK for downstream analysis. I am using bwa mem protocol.
As I was going through the options, I came across bwa mem -M option which is compatible with picard and GATK
-M mark shorter split hits as secondary (for Picard/GATK compatibility)
Can someone explain me what does this option do.
Also can bwa mem accept compressed .bz2 fastq files as input??
Hope to hear soon
Regards
Varun
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written
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Varun Gupta
without -M, a split read is flagged as 2048 (supplementary alignment) see http://picard.sourceforge.net/explain-flags.html. This flag is a recent addition to the SAM spec.
$ ./bwa mem ex1.fa <(echo -e "@R1\nATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAGGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTC\n+\nIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII") 2> /dev/null
@SQ SN:seq1 LN:1575
@SQ SN:seq2 LN:1584
R1 0 seq2 361 60 62M46S * 0 0 ATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAGGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 AS:i:62 XS:i:0 SA:Z:seq1,1273,+,60S48M,60,0;
R1 2048 seq1 1273 60 60H48M * 0 0 GATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 AS:i:48 XS:i:0 SA:Z:seq2,361,+,62M46S,60,0;
with option -M it is flagged as a duplicate flag=256 (not primary alignment): will be ignored by most 'old' tools.
$ ./bwa mem -M ex1.fa <(echo -e "@R1\nATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAGGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTC\n+\nIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII") 2> /dev/null
@SQ SN:seq1 LN:1575
@SQ SN:seq2 LN:1584
R1 0 seq2 361 60 62M46S * 0 0 ATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAGGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 AS:i:62 XS:i:0 SA:Z:seq1,1273,+,60S48M,60,0;
R1 256 seq1 1273 60 60H48M * 0 0 GATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 AS:i:48 XS:i:0 SA:Z:seq2,361,+,62M46S,60,0;
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Pierre Lindenbaum
Thanks Pierre
What does split read means here in context with -M option? So using option -M it says the read to be secondary alignment(not primary alignment) whereas without -M option it gives as supplementary alignment(2048).
What is the difference between "not a primary alignment " and supplementary alignment.
See the sam spec: http://samtools.github.io/hts-specs/SAMv1.pdf
An alignment of a read that cannot be represented as a linear alignment. A chimeric alignment is represented as a set of linear alignments that do not have large overlaps. Typically, one of the linear alignments in a chimeric alignment is considered the "representative" alignment, and the others are called "supplementary" and are distinguished by the supplementary alignment ag. A
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Pierre Lindenbaum
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hello ,-M means only one alignment displayed in sam file?