bam from samtools view -F 1294 is larger than bam from speedseq or

[liuhankui]

samtools view -F 1294 includes flag 2048 （supplementary alignment），but samblaster --discordantFile did not include flag 2048 （supplementary alignment），as well as speedseq， which used samblaster --discordantFile too. Is there a problem？

By the way, bwa mem mark supplementary alignment（flag 2048） reads as not primary alignment（flag 256） when using -M，mybe there will be another problem for someone who use bwa mem -M

[ryanlayer]

The current flags are the best option. The original wording on that -M option was confusing and our understanding if it evolved. We settled on not using -M and using the current flags.

On Nov 21, 2021, at 6:28 PM, Vincent @.***> wrote:

 samtools view -F1294 includes flag 2048 （supplementary alignment），but samblaster --discordantFile did not include flag 2048 （supplementary alignment），as well as speedseq， which used samblaster --discordantFile too. Is there a problem？

By the way, bwa mem marked supplementary alignment（flag 2048） reads as not primary alignment（flag 256） when using -M，mybe there will be another problem for someone who use bwa mem -M

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[liuhankui]

Many thanks for your suggestion.

I found different sizes of discordant bam files between samtools view -F 1294 and samblaster --discordantFile.

here is the commands:

bwa mem -R "@RG\tID:IDA\tPL:illumina\tPU:IDA\tLB:IDA\tSM:IDA\tCN:BGI" GRCh38.fa fq1.gz fq2.gz | samblaster --excludeDups --addMateTags --maxSplitCount 2 --minNonOverlap 20 -d samblaster.disc.sam -s samblaster.split.sam | samtools view -Sb -o sample.bam - samtools view -h -F 1294 sample.bam > samtools.disc.sam samtools view -h sample.bam | scripts/extractSplitReads_BwaMem -i stdin > samtools.split.sam

here is the differences: wc -l samblaster.disc.sam 121030 wc -l samtools.disc.sam 130582

wc -l samblaster.split.sam 34488 wc -l samtools.split.sam 36266

[ryanlayer]

That could just be samblaster removing duplicates.

On Nov 25, 2021, at 12:11 AM, Vincent @.***> wrote:

 Many thanks for your suggestion.

I found different sizes of discordant bam files between samtools view -F 1294 and samblaster --discordantFile.

here is the commands:

bwa mem -R @.***\tID:IDA\tPL:illumina\tPU:IDA\tLB:IDA\tSM:IDA\tCN:BGI" GRCh38.fa fq1.gz fq2.gz | samblaster --excludeDups --addMateTags --maxSplitCount 2 --minNonOverlap 20 -d samblaster.disc.sam -s samblaster.split.sam | samtools view -Sb -o sample.bam - samtools view -h -F 1294 sample.bam > samtools.disc.sam samtools view -h sample.bam | scripts/extractSplitReads_BwaMem -i stdin > samtools.split.sam

here is the differences: wc -l samblaster.disc.sam 121030 wc -l samtools.disc.sam 130582

wc -l samblaster.split.sam 34488 wc -l samtools.split.sam 36266

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