Hi Alec,

 

Sorry for the mistake, I used a wrong example. Here is another example:

The number of reads from BWASW aligned BAM (81635) is higher than the number of reads from the NOT aligned BAM (72578). So, the percentage of aligned reads is 112%!!!

The number of reads from BWAMEM aligned BAM (72059) is “logically” lower than for NOT aligned BAM (72578, again), 99%.

How do you explain the aligner BWASW can generate new reads?

Thanks for your answer!

 

Best,

 

Antony

 

--

Dr Antony Le Béchec

Institut Régional contre le Cancer (IRC)

Hôpitaux Universitaires de STRASBOURG (HUS)

Centre Paul Strauss (CPS)

Plateforme NGS - UF6434

Phone: +33 3 88 12 75 38

antony.lebechec@chru-strasbourg.fr

 

De : Alec Wysoker [mailto:alecw@broadinstitute.org]
Envoyé : lundi 7 juillet 2014 15:55
À : LE BECHEC Antony; bio-bwa-help@lists.sourceforge.net
Objet : Re: [Bio-bwa-help] Number of reads with BWASW higer than in the original FASTQ files!

 

Hi Antony,

Can you highlight the specific numbers that don't make sense to you?

Thanks, Alec

On 7/4/14, 7:38 AM, LE BECHEC Antony wrote:

Dear BWA members,

 

I’ve a question regarding the number of reads on aligned BAM.

I used Picard FastqToSam in order to generate an unaligned BAM file (14S0020.unaligned.bam, 660804 reads, corresponds to the number of reads in the 2 fastq). Then, I aligned this BAM using BWAMEM (14S0020.bwamem.bam, 660519 reads) and BWASW (14S0020.bwasw.bam, 650856 reads).

I obtain a strange number of reads for BWASW alignment, because higher than the original number of reads (see details below). Moreover, the stats from samtools are empty, conversely to the Picard HsMetrics stats (see below).

What do you think it happened with SW?

 

Thanks for your help!

 

Antony

 

Reads number calculation (samtools):

 

$ samtools flagstat 14S0020.unaligned.bam

660804 + 0 in total (QC-passed reads + QC-failed reads)

0 + 0 duplicates

0 + 0 mapped (0.00%:-nan%)

660804 + 0 paired in sequencing

330402 + 0 read1

330402 + 0 read2

0 + 0 properly paired (0.00%:-nan%)

0 + 0 with itself and mate mapped

0 + 0 singletons (0.00%:-nan%)

0 + 0 with mate mapped to a different chr

0 + 0 with mate mapped to a different chr (mapQ>=5)

 

$ samtools flagstat 14S0020.bwamem.bam

660519 + 0 in total (QC-passed reads + QC-failed reads)

0 + 0 duplicates

658154 + 0 mapped (99.64%:-nan%)

660519 + 0 paired in sequencing

330164 + 0 read1

330355 + 0 read2

654730 + 0 properly paired (99.12%:-nan%)

655787 + 0 with itself and mate mapped

2367 + 0 singletons (0.36%:-nan%)

759 + 0 with mate mapped to a different chr

351 + 0 with mate mapped to a different chr (mapQ>=5)

 

$ samtools flagstat 14S0020.bwasw.bam

650856 + 0 in total (QC-passed reads + QC-failed reads)

0 + 0 duplicates

650856 + 0 mapped (100.00%:-nan%)

0 + 0 paired in sequencing

0 + 0 read1

0 + 0 read2

0 + 0 properly paired (-nan%:-nan%)

0 + 0 with itself and mate mapped

0 + 0 singletons (-nan%:-nan%)

0 + 0 with mate mapped to a different chr

0 + 0 with mate mapped to a different chr (mapQ>=5)

 

Stats from Picard HsMetrics:

 

                               bwamem            bwasw

[+] Reads            660519                650856 

  PF/Aligned       100% / 99.53%                100% / 99.98% 

[+] Bases             162835277                        161277514         

  On/Off               99.9% / 0.1%                    99.89% / 0.11%

[+] Coverage     6213                    6154     

  > 30X                  100%                    100%    

  > 100X                100%                   100%

 

 

--

Dr Antony Le Béchec

Institut Régional contre le Cancer (IRC)

Hôpitaux Universitaires de STRASBOURG (HUS)

Centre Paul Strauss (CPS)

Plateforme NGS - UF6434

Phone: +33 3 88 12 75 38

antony.lebechec@chru-strasbourg.fr

 




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