bwa output

[scami]

Hi guys

I run bwa on my ILLUMINA reads with the following commands:

./bwa aln vitis12xCHR.fasta  s_1_1_sequence.txt -e 5  -d 0 -i 0 -t 6 >s_1_1_sequence.sai


./bwa aln vitis12xCHR.fasta s_1_2_sequence.txt -e 5  -d 0 -i 0 -t 6 >s_1_2_sequence.sai


followed by

./bwa sampe vitis12xCHR.fasta s_1_1_sequence.sai s_1_2_sequence.sai s_1_1_sequence.txt s_1_2_sequence.txt >s_1_bwaAlgnment.sam

If I open the resulting sam file I get the following output:

..........................................
ILLUMINA-C3C24B_0047:3:120:18879:10724#0	141	*	0	0	**0	0	CTAGCCCTAATTAAATTTATGTGTGACAATGTGCAAAATTTAGCACATTCAACCACAAAACTTCTATGAAGAGGT	aaaa\aaaaa_aa_aaaaa\aaaa[YWWPPHNNFOWUZ[[`a]]aaaaa`Q]KY^____[X_XXR^BBBBBBBBB
ILLUMINA-C3C24B_0047:3:120:18879:7314#0	77	*	0	0	*	*00	AATACGCCAAAAGTCTCNTCTCCTAACTNNAANTGGCAAAACTGNNGCTGAAGCTCATCCACTCCCTCTATGTCA	bbbabbbbbbbbbbb^`E``aaaaaWZXEEOODOO^]]``WWZWEDOOOONOOOOba^bbbbbbbbab[bBBBBB
ILLUMINA-C3C24B_0047:3:120:18879:7314#0	141	*	0	0	*	*00	ATATGGCGCGTCTGCACCAGGAGAAAGTGAGAGCTTATCTGACTTGCACACTATTCGATTATCCTATAAATCCTT	bbbb`bbabbabbbbbbbbbbb`bbbbc`X^``U`Ybb_bb`aPa_b`V`a`a\]J]\_\`\^XO^[M]Ya[a_a
ILLUMINA-C3C24B_0047:3:120:18879:10603#0	77	*	0	0	**0	0	TGTATTATGCTTATTAANGTTGATGANTNNTTNAAAGTTCTATTNNATTCAACCTTATTTCTTCCACTTTAAGCT	bbbbbbabbbbbbbb``E``[[[[[OEODDNODOONNOOONNNNDDOOOOOOOOObbbbbbbbbbbb_bb`_a^b
ILLUMINA-C3C24B_0047:3:120:18879:10603#0	141	*	0	0	**0	0	CAAAGGCTCATTGGCCTTTTATAAGGCGTCCCAACACTATTAAAATGAGGTCAAAAGTACCAAGTCTAAATTTTC	bbbbbbbbbbbbbbbbbbbbbbb^b\J`[WFNMOO`O```abW[_a_\aa_aUT_GNKOOXWFRQ^\T\V_^^V^
ILLUMINA-C3C24B_0047:3:120:18879:6287#0	77	*	0	0	*	*00	AACGATTATGATAACGGNAAAGGTAANANNAANGGTAATGATGANNGTAACAGTCACGGTCACAGTAATAGTGAC	bbbbbbbbbbbbbbbaaEaaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
ILLUMINA-C3C24B_0047:3:120:18879:6287#0	141	*	0	0	*	*00	CAGTTACCGTTACCGTCAATATAAACGTTACTATCACCGTTACCGTTATCGTCACCATTTCTATTACCGTCATCA	bbbbbbbbbabbbbbabb_bbbb_bbbab``bbbabbbbabbabaaaaaa]^aaaaa`aaa]aaZLZUUR`Z``^
ILLUMINA-C3C24B_0047:3:120:18879:15229#0	77	*	0	0	**0	0	AGAGGCCTCATGCATGGNTAGAAGATNCNNTGNGAGGAATCCAANNGAAAGAACATGACTAGCCTGCTGTTATAC	bbbbbbbbbbbbbbb^[E[[ONNNNNEODDNOENNZZX[YOOOODE]W]X``a__`bba[_b^__`Ua_[Z_\\Z
ILLUMINA-C3C24B_0047:3:120:18879:15229#0	141	*	0	0	**0	0	GAGAGCCTTCTCTAAGCTTCTTGGGTTGAGATTAGCTATTGAGTTGGAGATTCAAACCCTTTTGGAGGGATTGTA	bbbb^bbbbbbbbbbbZbbbbbbbbabbb`_b``bbbbbbbaa_aaabb_[a]ba_\bTaaa_a^YXX[[VTYTU
ILLUMINA-C3C24B_0047:3:120:18879:7980#0	77	*	0	0	*	*00	GTGGATTTGGTAGCTTANTTTTAAGANANNTTNAACAAATGAAANNGTTGTTTAGTTGCCCAACACACAATTTTT	_Y[_]_Z__BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
ILLUMINA-C3C24B_0047:3:120:18879:7980#0	141	*	0	0	*	*00	GTGGTTTAGCAAATGCTTCAGATGATGCTCGAAGATCGAGCCAGAGGCAGGCTATCTTTGTAGAAGACAACGCTG	XPRZJ]YQ[[`__\`````___```^]aaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
ILLUMINA-C3C24B_0047:3:120:18879:9103#0	77	*	0	0	*	*00	GTTCCACTTTTGGAAGANCCTGCGTTNTNNCANCAGATCTTGATNNTTCATATATAAATGTAACTAATGTATCTC	bbbbbbbbbbbbbbbbbEbb^^^^^ODNDDNOEOO`^`^`NNOOEDOOOO`^^``bbbb``b\abbab`_bb`\_
ILLUMINA-C3C24B_0047:3:120:18879:9103#0	141	*	0	0	*	*00	TATTTGTGAAAATGTATGTATAGCCAAAAAAGGACCACACCTAAAATCAGGTCAAGTTCTAATTGTTCAAGTTGA	bbbcbbabbbbbbbbbbbbbbbbbbbbbbXHWFVXYYYY[^bb\b_\`bb__^b_\\``]bab^_``aaa_^Y__
ILLUMINA-C3C24B_0047:3:120:18879:8267#0	77	*	0	0	*	*00	AATGATAGAATGAAGAANTGCTCCCCNANNGTNTTCCGGACCTCNNTGTTGGGGGAGAAGGTCGCCGTGTTCTGT	bbbbbbbbbbbbbbbBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
ILLUMINA-C3C24B_0047:3:120:18879:8267#0	141	*	0	0	*	*00	ATTCGATTTCGCCTAAATTATAATTTATGATAATAAATATATCAATTTGATGATTTAAGTGCAACGCCTTTGGGG	bbbb^b`bbbbbbbbb_bbbbbbbbVVWUVLVWVW]VYY]bbbabbbb]baa\`a]`^````[\\`[Z``b_Y^B
................................

I thought I was supposed to have in each single line also the position on chromosome and the cigar field with the informaiton about snp and indels. Am I doing anything wrong?

thanks four your help

[drio]

For those reads you are showing BWA could not find alignments. That's why you don't see the chrm or any other mapping information.

BWA will not call SNPs for you, it only find the best alignments for your short reads. You need a different tool to perform the SNP calling. The two most used tools are samtools (same author than BWA) and the GATK framework from the BI.