Sorted bam

[wangzkai]

I have a bam file which were already sorted (by coordinates) using "samtools sort". However, when I tried to remove duplicate reads using picard's "MarkDuplicates" function, it failed saying that the input bam was not sorted according to the headers. So my questions are the following:

1. Why a bam file sorted by samtools considered not sorted by picard?
2. How can picard tell whether a bam file is sorted or not from the headers?

Thanks for any help on this!

[nilshomer]

I have a bam file which were already sorted (by coordinates) using "samtools sort". However, when I tried to remove duplicate reads using picard's "MarkDuplicates" function, it failed saying that the input bam was not sorted according to the headers. So my questions are the following:

1. Why a bam file sorted by samtools considered not sorted by picard?
2. How can picard tell whether a bam file is sorted or not from the headers?

Thanks for any help on this!

Samtools does not modify the header correctly. You can use Picard to sort in the future. Use the "AS=true" option when running "MarkDuplicates" to override the header check.

[maubp]

Have you reported this possible bug in samtools?

(I'm interested since I have some BAM files sorted with samtools which are causing problems in a Picard based viewer)

[nilshomer]

Have you reported this possible bug in samtools?

(I'm interested since I have some BAM files sorted with samtools which are causing problems in a Picard based viewer)

The samtools developers are aware, but recommend using Picard as this probably wont be fixed anytime soon. I am sure if you give some of your grant money they would be happy to help .