Integrate read end clipping in to allelecounter #60

danchubb · 2019-11-22T13:40:23Z

alleleCount-FixVAF is a fork which includes a "-e n" parameter which ignores all sites within n bases of the end of the read.

This is to correct an issue with reference bias in the illumina Isaac aligner described in https://www.biorxiv.org/search/chubb%252Bcornish

The default -e is 5. Might be worth changing it to 0 if it was to be rolled in to the main allelecounter.

make sure that qpos and length are what they think. If they are position on read and length of read, next step is to skip if position <=n or >= length -n printf("Read posis %d\n" , p->qpos); printf("Read posis %d\n" , p->alignment->query->length);

add end clip option

simplified to just skip the whole step if the variant is in the final or first 5 bases.

Added comment pointing out default setting. We use 5 for the illumina data but if it was to be used optionally, setting it to 0 would make more sense.

danchubb added 29 commits October 21, 2019 12:55

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make sure that qpos and length are what they think. If they are position on read and length of read, next step is to skip if position <=n or >= length -n printf("Read posis %d\n" , p->qpos); printf("Read posis %d\n" , p->alignment->query->length);

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simplified to just skip the whole step if the variant is in the final or first 5 bases.

Update bam_access.c

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Added comment pointing out default setting. We use 5 for the illumina data but if it was to be used optionally, setting it to 0 would make more sense.

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Integrate read end clipping in to allelecounter #60

Integrate read end clipping in to allelecounter #60

danchubb commented Nov 22, 2019

Integrate read end clipping in to allelecounter #60

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Integrate read end clipping in to allelecounter #60

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danchubb commented Nov 22, 2019