SOAP aligner output format? and composite quality scores?

[RLamb]

Hi,

could someone please tell me what the output of SOAP aligner looks like (e.g. one sample line, with explanation of what the various items are). The thing is, I want to feed it into SOAPsnp, but I can't use the aligner cause its executables run only on a Unix platform which I don't have (easy) access to (the snp program comes as source code, but I'm not proficient enough in C to sort through it and see what input it takes). I've tried extracting the alignments from my bowtie .map file and reshuffling them in various ways like <position> \t <sequence> \t <quality string> \n, but soapsnp always gives a "Bus error".

On a related matter, does anybody know of a simple, intuitive metric for the quality of a consensus sequence? For example, if a given position (in haploid DNA from a single source, so the real sequence is a single allele) is covered by 5 reads, and it reads A in 3 of them with Phred scores of 15, 25 and 30, and G in the other two with qualities 20 and 30 - what is the probability that the actual sequence is A? What that it's G?

Thanks!

[jayce_ocean]

SOAPAligner output format

hi

i am interested to know the SOAPAligner output format..can anyone share it?thanks..

[ormium]

http://soap.genomics.org.cn/soap1/#Formatofoutput



Romeo Kienzler
r o m e o ( a - t ) o r m i u m . d e

[ormium]

And here is an example (made by hand, so not sure if it is correct):

10 AAAGTCAATTATCAAGTTGAACCAGCTCGTGTTGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 37 a 37 + Streptococcus_suis 86299 0
15 AGCTAGTCCCGAAGAAAATCTAGGTGGAATCGGGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 37 a 37 + Streptococcus_suis 142141 1 C->35G30
13 TGGTTTTGGTGGTATCGGTGGAGAGTATATCAAGCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 37 a 37 + Streptococcus_suis 241778 0
2 CAAGAAATCGGTGTGGCAGAAGCCTTTACAGCGGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 37 a 37 + Streptococcus_suis 297899 0
12 AAAATTGCATAAAATAGGTAGCTAGCTCTGCTAGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 37 a 37 + Streptococcus_suis 397758 0
8 AGCTTTAATATCTATATTAGTGGTATTGATGCTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 37 a 37 + Streptococcus_suis 553513 0
14 GGAAGAAGAAGGAAATCAAGAAGGGAATAATATAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 37 a 37 + Streptococcus_suis 626711 0
1 GCCTGTTCTTTACATGATTTTTGGTCTAGTGTATGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 37 a 37 + Streptococcus_suis 766133 1 A->31T30
11 GATTACTTGTAATTATACGTTACAAAATCATATTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 37 a 37 + Streptococcus_suis 1503808 2 A->30T30 A->32T30
9 AGACTTAACCCAACAACTTTTTGAATTAAGCGAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 37 a 37 + Streptococcus_suis 1779842 0