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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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head instead of tail ? #302

Closed lindenb closed 5 years ago

lindenb commented 5 years ago

related to https://github.com/arq5x/lumpy-sv/issues/235

in the recommandation: https://github.com/arq5x/lumpy-sv#lumpy-traditional , it is said:

samtools view -r readgroup1 sample.bam \
    | tail -n+100000 \
    | scripts/pairend_distro.py \
(...)

shouldn't it be (head instead of tail) ?

samtools view -r readgroup1 sample.bam \
    | head -n 100000 \
    | scripts/pairend_distro.py \
(...)
ryanlayer commented 5 years ago

Since the BAMS are sorted, the beginning of a BAM contains reads from messy areas of the chr1. We use tail to try and skip these.

On Fri, Apr 19, 2019 at 6:13 AM Pierre Lindenbaum notifications@github.com wrote:

related to #235 https://github.com/arq5x/lumpy-sv/issues/235

in the recommandation: https://github.com/arq5x/lumpy-sv#lumpy-traditional , it is said:

samtools view -r readgroup1 sample.bam \ | tail -n+100000 \ | scripts/pairend_distro.py \ (...)

shouldn't it be (head instead of tail) ?

samtools view -r readgroup1 sample.bam \ | head -n 100000 \ | scripts/pairend_distro.py \ (...)

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lindenb commented 5 years ago

Ahh got it , thanks !