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Fix additional broken links due to org LINK parsing
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chapmanb committed Aug 31, 2015
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8 changes: 4 additions & 4 deletions posts/hg38_validation.org
Expand Up @@ -185,7 +185,7 @@ discordancy:
Both hg38 and hg38_noalt (without alternative haplotypes) have improved
detection of SNPs and indels compared to hg19. The full hg38 also demonstrate a
reduction in false positives relative to hg38_noalt, showing the advantage of
alternative haplotypes for resolving mapping issues. The [[fb_platinum-plot][FreeBayes calls]] look
alternative haplotypes for resolving mapping issues. The [[fb_platinum_plot][FreeBayes calls]] look
similar and resolve slightly better than GATK with more concordant SNPs
and indels.

Expand Down Expand Up @@ -248,11 +248,11 @@ caution in interpreting results.

#+LINK: val_album http://imgur.com/a/2Ezon
#+LINK: joint_val http://bcb.io/2014/10/07/joint-calling/
#+LINK: heng_38-val https://github.com/lh3/bwa/blob/master/README-alt.md#preliminary-evaluation
#+LINK: heng_38_val https://github.com/lh3/bwa/blob/master/README-alt.md#preliminary-evaluation
#+LINK: freebayes https://github.com/ekg/freebayes
#+LINK: gath_hc https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php
#+LINK: bwa https://github.com/lh3/bwa
#+LINK: fb_platinum-plot http://i.imgur.com/byZN0kY.png
#+LINK: fb_platinum_plot http://i.imgur.com/byZN0kY.png
#+LINK: giab_paper http://www.nature.com/nbt/journal/v32/n3/full/nbt.2835.html

* Scripts, chromosome naming and future work
Expand Down Expand Up @@ -290,7 +290,7 @@ regions with multiple alternative alleles. hg38 is a great first step in moving
towards a more accurate, graph-based, representation of human heterogeneity.

#+LINK: hg38_scripts https://github.com/hbc/giab_remap_38
#+LINK: bcbio_38-val https://bcbio-nextgen.readthedocs.org/en/latest/contents/testing.html#human-genome-build-38
#+LINK: bcbio_38_val https://bcbio-nextgen.readthedocs.org/en/latest/contents/testing.html#human-genome-build-38
#+LINK: hg38_naming ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/README_ANALYSIS_SETS
#+LINK: ucsc_naming https://www.biostars.org/p/94826/#116487
#+LINK: vg https://github.com/ekg/vg

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