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 _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_samtools-2Dhelp&d=DwICAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=iKRz7N6xL3uJ6tuuPlViiQ&m=0kLKTaWw64WzDI-r_NaNQe-kuhVK6-i45wu_xTrFbHc&s=wI5YAPkY6Dsh1-uBTLHC1o4h_g_mIHjafOgi1cFMAY0&e=
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