Description
A track showing the regions of CHM13 with no primary aligments from GRCh38 (excluding patches/alts/chrY)
Methods
The track was generated using Winnowmap v2.0.1 with the command: winnowmap -ax asm20 -H --MD chm13.v1.0.fasta GCA_000001405.28_GRCh38.p13_genomic_noalt_noY.fasta , primary alignments were converted to paf and filtered for primary only via k8 paftools.js sam2paf -p out.sam and converted to unmapped regions by inverting the list of mappings w/MAPQ greater than 0
cat out.paf |awk '{if ($12 > 0) print $6"\t"$8"\t"$9}'| bedtools sort -i - | bedtools merge -i - | bedtools complement -i - -g chm13.v1.0.sizes
and likewise for v1.1 assembly.
Display Conventions and Configuration
Data access
Release history
- 2021/05/24, Winnowmap uncovered track for chm13.v1.0 assembly.
- 2021/05/24, Winnowmap uncovered track for chm13.v1.1 assembly.
Contacts
Credits
Please cite Winnowmap
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