Soap Result Converted To Bam Not Working In Samtool

Question

[Sarwar]

I converted the output of soap2 which is map file to sam file using map2sam.pl and then converted this sam to bam using samtools again sorted this bam then pileup. finally i could net get any result in snp file produced from bcftool. can any body help? Thanks in advance

[Istvan Albert]

Not being able to call SNPS does not mean that the file is "not working". First collect some information on you bam file. How many reads map correctly etc. Then you would need to show the commands that you are trying to run.

[Torst]

What does "wc -l file.sam" say? This counts the number of lines in your SAM file, which is roughly how many mapped reads you got.

[lh3]

Once you can convert to BAM, the soap2->sam conversion is fine.

Answer 1

[Yintze]

Hey I am interested to know if this has been sorted out yet? As I am facing the same problem as well.

These are the commands that I used:-

soap index

2bwt-builder ref.fa

soap alignment

soap -a read1.fq -b read2.fq -D ref.index -o map.file -2 unmap.file -m 300 -x 500

Instead of using the map2sam.pl file, I used the soap2sam.pl file

sam2bam

samtools faidx ref.fa

samtools view -bt ref.fai -o read.bam read.sam

bam2sorted

samtools sort .bam .sorted

merge

samtools merge merge_read.bam bam1 bam2

pileup

samtools mpileup -ugf ref.fa merge_bam |bcftools view -bcvg -> merge_bcf

bcftools view merge_bcf >merge_vcf

This is one of the result from my flagstat file:- (my original file has 364617084 reads)

66478440 + 0 mapped (100%:nan %)

66478440 + 0 paired in sequencing

33239220 +0 read 1

33239220 +0 read 2

0 + 0 properly paired (0.00% :nan%)

66478440 + 0 with itself and mate mapped

0 + 0 singletons (0.00% :nan%)

0 + 0 with mate mapped to a different chr

0 + 0 with mate mapped to a different chr (mapQ>=5)

I'd love to hear some inputs. It seems like all of the mapping distributions for my paired-end test files on SOAP2 are 0% when it comes to being properly paired. Any idea what could go wrong?

Thanks a bunch!

Yintze

[lh3]

Please post this as a separate question. Thank you.

[Michael]

Actually, there is no problem here. The original poster states there is not snp called, but that doesn't mean that the pipeline doesn't work.

Answer 2

[Yumtaoist]

I have reviewed the sam file that converted from soap result and compare it to the sam file generated by bowtie2. I found that the result of soap have lost some information such as "AS, XN, XO, XG, etc.". Perhaps this is the reason.