soap3-dp and samtools fail to list variants

[robertthebob1]

Here is an example of both soap3-dp and bowtie2 alignments and variant calls on lambda_virus.fa. Before I dig any further, does anyone have a solution to this problem, that the vcf results from soap3-dp+samtools does not include the lambda_virus sequence and prints the N in its place.

#Build the 2BWT index
soap3-dp-builder lambda_virus.fa
#Convert the 2BWT index to the GPU-2BWT index
#However, samtools variant call fails either way.
BGS-Build lambda_virus.fa.index
#Align the unpaired reads to the genome
soap3-dp single lambda_virus.fa.index reads_1.fq -b2 # make sam output
merge-sam.sh reads_1.fq
samtools faidx lambda_virus.fa
samtools view -bS -t lambda_virus.fa.fai reads_1.fq.out > eg1.sp.bam
samtools sort eg1.sp.bam eg1.sp.sorted
samtools mpileup -uf lambda_virus.fa eg1.sp.sorted.bam | bcftools view -bvcg - > eg1.sp.raw.bcf
bcftools view eg1.sp.raw.bcf > view.sp.txt

bowtie2-build lambda_virus.fa lambda_virus
bowtie2 -x lambda_virus -U reads_1.fq -S eg1.bt.sam
samtools view -bS eg1.bt.sam > eg1.bt.bam
samtools sort eg1.bt.bam eg1.bt.sorted
samtools mpileup -uf lambda_virus.fa eg1.bt.sorted.bam | bcftools view -bvcg - > eg1.bt.raw.bcf
bcftools view eg1.bt.raw.bcf > view.bt.txt
head -40 view.sp.txt view.bt.txt

==> view.sp.txt <==
...
ref|NC_001416.1| 1 . N G 55.3 . DP=6;VDB=2.753126e-02;AF\
1=1;AC1=2;DP4=0,0,1,4;MQ=33;FQ=-42 GT:PL:GQ 1/1:88,15,0:27
...

==> view.bt.txt <==
...
gi|9626243|ref|NC_001416.1| 2 . GGCG GGCGCGGGGGCG 3.81 . INDEL;IS\
=1,0.250000;DP=4;AF1=1;AC1=2;DP4=0,0,1,0;MQ=40;FQ=-37.5 GT:PL:GQ 0/1:39,3,0:4
...