SOAP aligner output format? and composite quality scores?

RLamb · 08-18-2009, 04:48 PM

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 · 09-07-2010, 07:15 PM

hi

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

ormium · 08-30-2011, 09:04 AM

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 · 09-09-2011, 06:20 AM

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

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08-18-2009, 04:48 PM	#1
RLamb Junior Member Location: NH Join Date: Aug 2009 Posts: 1	SOAP aligner output format? and composite quality scores? 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!

09-07-2010, 07:15 PM	#2
jayce_ocean Junior Member Location: location Join Date: Sep 2010 Posts: 5	SOAPAligner output format hi i am interested to know the SOAPAligner output format..can anyone share it?thanks..

08-30-2011, 09:04 AM	#3
ormium Junior Member Location: basel , switzerland Join Date: Aug 2011 Posts: 3	http://soap.genomics.org.cn/soap1/#Formatofoutput Romeo Kienzler r o m e o ( a - t ) o r m i u m . d e

09-09-2011, 06:20 AM	#4
ormium Junior Member Location: basel , switzerland Join Date: Aug 2011 Posts: 3	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