samtools mpileup

[hv4]

Hi,

I am using the following command

(samtools view -bS $prefix.out.sam > $prefix.out.bam
samtools sort $prefix.out.bam $prefix.out-sorted
samtools rmdup $prefix.out-sorted.bam $prefix.out-sorted-NoDup.bam


samtools mpileup -ugf HumanRef-hg19.fa $prefix.out-sorted-NoDup.bam | bcftools view -bvcg - > $prefix.var.raw.bcf
bcftools view $prefix.var.raw.bcf | vcfutils.pl varFilter -D 100 > $prefix.var.flt.vcf
) &

to find SNPs with samtools mpileup.

All $prefix.out-sorted-NoDup.bam files get generated OK.

The problem I have is that the *.vcf files contain only chromosomes 1 to 3.

What can be the cause of this?

Thank you.

[Heisman]

Do your reference sequences and aligned files contain more than chr 1-3?

[hv4]

Yes, that is correct the samples and the reference contain all chromosomes.

The interesting thing is that I am running 8 samples in parallel and the results for all of them contain only chr1-3.

Now, I ran the same code on another set of 8 samples, also in parallel, and the result are from chr1 to chr13! The samples contain all chromosomes.

I noticed something interesting: the bcf file for sample 7 grew in size very rapidly while the others were very slow in comparison.

I used "kill -STOP procid" to stop the process for sample 7 and the bcf file stopped increasing in size while the others did not speed up.

The reason I did this was to see if it has something to do with running all samples in parallel in the same directory.

Maybe I should use the multiple file option and see if I get the same results.

Anyway, the bcf file for sample 7 got to be 3.3GB while the others only about 40MB. Also the vcf for sample 7 contains only the header!
The others have info for chr1-13.

Also, the ID field contains a dot for all rows. Could this mean that samtools is not configured properly?

Thanks.