BWA - XM tag Question

[Arupsss]

I have installed BWA. And build index of hg19 using command:

bwa index -a bwtsw hg19.fa

Now I find alignment using command:

./bwa aln hg19.fa SRR4493095_1.fastq > aln_sa.sai

However, I want to find alignments allowing 1 or 2 mismatches.

From BWA home page, I found, I have to use XM tag.

But, can't get how to use that means what should be the command.

Can anybody please help me on this ?

Thanks.

[Arupsss]

Another point is that, in some places I found - n 0/1/2 this tag gives specified number of mismatch. However, can't understand whether is that true or not. Little bit confusing because some places told to use XM (but don't specify how) some places told to use - n 0/1/2 .

[xied75]

You misunderstood the XM tag, XM IS a TAG in the output of BWA SAMPE/SAMSE step (which is a SAM file).

-n IS a switch (or options/parameters) when you run BWA, there are many switches you can give.

With default values for these (i.e. don't use them at all) you already can have 1 or 2 mismatches.

[Arupsss]

You misunderstood the XM tag, XM IS a TAG in the output of BWA SAMPE/SAMSE step (which is a SAM file).

-n IS a switch (or options/parameters) when you run BWA, there are many switches you can give.

With default values for these (i.e. don't use them at all) you already can have 1 or 2 mismatches.

Thanks for reply:

Actually, I am comparing, BWA vs BowTie. For, BowTie, I can specify output allowing mismatch by command

./bowtie --all -v 0 hg19 SRR4930952.fastq SRR4930952.txt (v specify number of mismatch).

I want same command to compare with BWA ( it's paper say's, it allows).

So, what command should I give to find exact matches and allowing 1/2 mismatches (I am using 150 bp read).

[xied75]

-k and/or -n. -k is mismatch in seed, -n is overall, not sure what combination you need with your 150bp read.

[Arupsss]

-k and/or -n. -k is mismatch in seed, -n is overall, not sure what combination you need with your 150bp read.

I have no restrictions in maximum edit distance in the seed.

Can you inform me: what does this - n option means.

It says:

-n NUM Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]

So, if I run in default setting for 150 bps read, it allows 6 mismatches ?

And for allowing no mismatches:

I have to set - n 0.

For 2 mismatches for 150 bps,

I have to set - n 2.

Is this correct ?

[xied75]

Yes, -n 0 for all match, -n 2 for 2 mismatches.

[Arupsss]

Yes, -n 0 for all match, -n 2 for 2 mismatches.

Thanks a lot. This I want to make sure. And by default:

it gives

[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9

mismatches ? True ?

[xied75]

Yes that's the default output you see when there is no -n used.