[Samtools-help] Sort and rmdup

[Henrikki A. <hen...@he...>]

Hi,

I've tried to use the piping from sort but it seems to fail. If I run
the two commands:

samtools import ensembl-hs_GRCh37_56.fa.fai alignment-raw.sam - |
  samtools sort - raw-sorted
samtools rmdup raw-sorted.bam sorted.bam

This produces a 1.8Gb sorted bam file. However if I try to use the
piping the sort:

samtools import ensembl-hs_GRCh37_56.fa.fai alignment-raw.sam - |
  samtools sort -o - raw-sorted | samtools rmdup - sorted.bam

I get 163 Mb bam file. What causes the difference?

Thanks,
-- 
Henrikki Almusa