After doing Bowtie2 alignment I ended up in less data.

[ssn4ssn]

I am having single end sequence data from Illumina and did the mapping using the Bowtie2 default parameters. Then I converted it to bam format from sam format using samtools view -bS ....sam > .......bam
Then I sorted the bam file using
samtools sort ........bam .....sorted
Then I used samtools
samtools mpileup -uf hg19.fa .......sorted.bam | bcftools view -vcg - > ......vcf
Then when I saw the result in the vcf format, I was able to see only chr 1,2,3,4,
I was not able to find the variations in rest of the chromosomes.

The data is of a human single cell.
Any idea why i got only SNPs and INDELs for first 4 chromosomes. I am not sure where I went wrong and also I have used default parameters everywhere possible.
Any ideas or answers are welcome. Thanks in advance.

[dpryan]

Did you look at the original SAM file to make sure it contains all of the reads? There were some bugs in the previous version of bowtie2 (-beta5 I think) that caused it to stop alignments early. If not, it might be helpful to just browse through your data and have a look to make sure that things look OK.

[ssn4ssn]

Thanks dpryan. I am using the beta 6 version of Bowtie2. I had a quick look at the sam file but was not able to find any missing information and the file is also big. I would now have a more deeper look into the same and will let know if I can find some difference from normal.
Once again thanks for the reply.
I have checked again with the sam file using BWA instead of Bowtie2 and both the .sam files same data with some differences at the end of each read quality. But otherwise everything looks fine.

[arvid]

You can checking mapping in a BAM file with "samtools idxstats file.bam"; that will tell you the number of reads mapping to each chromosome.
If the mapping looks fine, try breaking up all the further steps into single program steps, saving the output every time, and checking it for completeness. A quick-and-dirty simple check for the bcf/vcf files would be to cut out the column with the chromosome, e.g. something like "cat file.vcf | cut -f 1 | sort | uniq" on a VCF, exchanging "cat" with "bcftools view" for BCF files.

[ssn4ssn]

Thank you Arvid. I will try it.