Dear Andrew,
Thanks.
On 16.07.20 13:22, Andrew Whitwham wrote:
Hi Nadia,
samtools stats counts duplicates using the duplicates flag. If no other
filtering is done while running stats then the count will include duplicates on
supplementary and even unmapped reads. So your calculations are probably
removing the same reads twice.
Andrew
________________________________________
From: Nadia Baig <ba...@hhu.de>
Sent: 16 July 2020 11:57:14
To: Andrew Whitwham; samtools-help@lists.sourceforge.net
Subject: Re: [Samtools-help] samtools stats [EXT]
Dear Andrew,
I used picard.
On 16.07.20 12:41, Andrew Whitwham wrote:
Hello Nadia,
What did you use to mark the duplicates in the first place?
Regards,
Andrew
________________________________________
From: Nadia Baig <ba...@hhu.de>
Sent: 16 July 2020 10:22:07
To: samtools-help@lists.sourceforge.net
Subject: [Samtools-help] samtools stats [EXT]
Dear support team,
I have 10x genomics data set (paired-end). After alignment I used
samtools to get stats.
Following are the statistics:
Total reads: 622018758
Paired in sequencing: 311009379
Mapped: 596403847
Unmapped: 25614911
Duplicates: 111855687
properly paired: 415286153
Non-primary alignments: 44200142
reads MQ0: 22973571
It means : 622018758-25614911-22973571-44200142-111855687=417374447 are
the unique reads in this sample.
I am using following command to get the uniquely aligned reads:
samtools view -q 1 -F 4 -F 256 -h $input_bam | grep -v -e 'XA:Z:' -e
'SA:Z:' | samtools view -b > $path/output_filtered.bam
and results are ( unique reads) = 412805249 and it does not match the
above calculations.
I used sambamba tool too with the following commands:
sambamba view -t 12 -h -f bam -F "mapping_quality >= 1 and not (unmapped
or secondary_alignment) and not ([XA] != null or [SA] != null)" $input2
-o $path/Felsina-uniq.bam
results =412805249 unique reads
I used picard to remove duplicates. Is there any difference between
samtools duplicates detection and picard?
Looking forward to hearing from you soon.
Best wishes,
Nadia
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