Skip to content

Instantly share code, notes, and snippets.

View amwenger's full-sized avatar

Aaron Wenger amwenger

28 followers · 0 following
View GitHub Profile
@amwenger
amwenger / pacbio-paftools.vcf
Created March 1, 2019 23:15
Test dataset for truvari --multimatch extension
This file has been truncated, but you can view the full file.
##fileformat=VCFv4.2
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
@amwenger
amwenger / tr.bed
Created November 24, 2018 08:05
Tandem repeat BED file created by SMRT Link 6.0 for GCA_000001405.15_GRCh38_no_alt_analysis_set
This file has been truncated, but you can view the full file.
chr1 10000 10468
chr1 10627 10998
chr1 11224 11448
chr1 19305 19443
chr1 30867 30948
chr1 33449 33541
chr1 52137 52237
chr1 54712 54817
chr1 66157 66632
chr1 83505 83682
@amwenger
amwenger / sort-error.fofn
Last active November 21, 2018 06:44
Test dataset for SURVIVOR sort error
sort-error.vcf
@amwenger
amwenger / eqxread.fa
Last active June 4, 2018 18:01
Test case for minimap2 --eqx bugfix
>m141225_192409_42156_c100747972550000001823169907081546_s1_p0/9890/2369_12657
CCAAGCGCTGTAGATTGAGTGTCGCAGCGTCGGTTGTGAATCTCAATCTCAGGAGGCTTAGATCTGTCTGAGGATTATAAATGGTGGCGCTATACCAAAAAACTATAAGATCATCGGATCTACACGATACAGGGATATGATTGGTTGAGGTGTTCAGTCCACCATTCCATATACAAAATGTGGCTTTAATTCGATTTTAATGCTGGCCACAGTACAGCAAATAAATGAAGTTCATATCAGCACACTTCCGTTATATGGGTGGCGTTCAGGAACCGGTACAACGACTCATTGCGCTGCCCCAGAGAAGCGGTTCCTGAGTGAGCTGCTCACATCTACCACCTTGGTCCTGCTCACCTTTTTCTCCTCCCGCTCTCCTCCCCCAACCACTCTGATCACTCCCTTCGCTACAAATTCCCCTGCGATGGGACACACTAGCACTAGCACTGTCCACATGAGGGTTTAGTCTGGTCCCTCCACCTTATAAAAGATTTCTAATACCAGTCAAATTATGCGCTGATCAGTTTTCAGATGTTTTAAAAATCTCAATAGAGCTGTCTTCAAATTGTAACAAGACATTTACTCATAAGAATAGAGAATTAAAATAATACGATCGATGGTCAGGAACAATTCCAGGAGGAACCAAGAAAAATGAAAAAGCACATATAGGGTGGATACTCTCCTGATCCTGAAATTGCAACTTTAGTCTATTAGGTTTTTTTGTTTTTGTTCTTTGGAGGCAGAGTCTCAACTCTCCGCAGGCTGGAGTGTAGTGCTGCGATCTTCACAGCTGCACTGAACCTCGTCTCCTGGGTTTTAACGGCGATTCTCCTGCCTCAGCCTCTACCGAGTAGGTCTGTGGATTAAAGGCACTGCCACCTTATGCCTTGCCTATATTTTTGTACTTTTTAGTTAGAGAGAGGTTTCACCATGTTGGCCAGGCGTCTT
@amwenger
amwenger / hg19.nochrXInHeader.sam
Last active May 16, 2017 00:09
hg19 no chrX in header BAM test
@HD VN:1.0 SO:coordinate
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@amwenger
amwenger / ce.test.sam
Created May 16, 2017 00:04
C. elegans BAM test
@HD VN:1.0 SO:coordinate
@SQ SN:I LN:15582116
m141231_011325_42163R_c100748692550000001823169907081500_s1_p0/159404/14786_24486 2048 I 10001 0 304S16M1I2M1D2M1D5M2D10M1D21M1D3M3I14M1D13M1D3M1I11M1I3M1I9M1D10M2I3M1D11M1I5M1I7M1I3M1I16M1I5M1D6M1I9M1D5M1D16M1D5M9168S * 0 0 CCTAACTCTAACCCTAACCTAACCATGTAACGCCTAACCTAACCCTAACCCTAACCATAACCCTAACGCCAACCCACCCAACGCTAACCCTAACCCTAACCCAACCCCAACCCCACCCAACCCCACCCCAACCTAACCCCTAACCCTAGCCCTAGCCCTAGCCCTAGCCTAGCCTAACCTAACGCCTATAACCTGAACCGCTATACCCCTAACCTTAACGCTTAACCTAACCCTAACCCTAACACCTAAACTACGACCTTAACCCTAGCCTAGCCCTAGCCCTAGCCCTAGCCTAGCCTACCCATAACCCTAACCCTAACGCCAACCTAACTAACCCTAACCTAACCTTAACCCTAACACTACCAAACTAACCCTAACCCTACCCTCACCCTAACCTAAACCCTATCCCTATCACCTAACACTACCCTAACCCGCTAACCTAACCCTAACCCCCTAAACCCTATACCTCTAACCCTAACCCTAACCCTAACCTAACACCTAACCCTACCCTACCCTCACCCTAACCCAACCCCACCCCGCAACCCACGCCCAACCCCAACCCAACCCCAACCCTTAACCTTAACCCTTAACCCTACCCTAACCTTAACCGCATAACCCTAACGCCTCACCTAACCCCTAAGCCCTAACCCTAACCCTAACCCTAACCCCAACCCAACCCTAACCTATACCTAACCCTAACCCTACCTAACTCTAACCTCAACCCAACCCTACCCTAACCTACGCCTAACCGCC
@amwenger
amwenger / test.fa
Created April 21, 2017 22:51
>1
AAAGGGGGTTTCGCCATGTTGGCCATGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCTGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAG
CCACCGCACCCGGCCGCAGAGATAAATTTAGATAATGCATATCAAGTGCCTAGCACAGTATTTGTCACGTGGTAACAATTCAATTATGTATTTTATTCAT
CAGAGAAGATTCCAGGTAACTTTACCTCAAAGGGCAAAGTTTCCTCATCACTCAGGATATTCTTACAGAATTAATCATAGGCTTTGAAGGCAAAAGCAAA
TCAAAGGGTACAAAAATTTTACTGGTACAAAACAGAAAAAGGAGACTGACCAAAGTGGCTAGTCTGAGAGAAAAGTAGGTTCCTGGATAAGGAAATCAAG
CTAAGTACTTTTAAGACTAATCGTAATTCTTAAATACTATAAAAGAAACACATCGGCCAGGCTTGGCAGCTCATGCCTGTAATCCCAGCACTTTGGGAGG
CCGAGGCAGGAAGATCACCTGATGTCGAGAGTTCAAGACCAGCCTGGCCAACATGGCAAAACCCCATCTCTACTAAAAAATACAAAAATTACCCAGGCAT
GGTGGCAGGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGGAGAATTGTTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCTCACCAC
TGCACTACAGACTGGGTGACAGAGCGAGACTCCATCTCAAAAAAAAAAAAAAAAACACATCAAAAATCTTTTTAAAAATTTCTCCTATCTGTTCAATTTC
TTGAGACTGAAACAAAATAAAATGTTATTACAAGTAAGATGTTTCCAGCATATTTAAGAACAAAACCATATTTAATTTTCTTTAAAAAAATAGGGGGAAA
@amwenger
amwenger / 20388_33105.fa
Created March 6, 2017 18:09
Test files for NGM-LR "no primary" bug
>m54026_160803_070612/28836180/20388_33105
AAATGTTAAATAGAGCAGTGGCTAAGTAAAACAAACAAACAAACAAAAACAACAGCAACAACAACAAAACAGAAAATATCAACTTCTGGTAATCATCTTAACTTGAACCAGATGTTAGAAGAAATGGATATCGGCTGGGAGTGCGGTAGCTCATGACTGTAATCCCAACTTTGGGAGGGACTGAGGCGGGTGGATCACTTGAAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGGAAAACCGGTCTCATACTAAAAATACAAAAATTAGCTGGCGGGGTGGTGTGTGCCTGTAATACCAGGACCACCTCCACACCTCAGCCTCCCAATCCCACTCCCACGTCAGCTGAGGCTGCAGTGAGCATTGAATCACACCACTTTACACCGCTGGGGGACAGAGTATAGAAACGGTCTAAAAACAACAAAAAAGAAATGGCTATCATGGATATAATGAAGAAATAAAAGTTTATTATGTATTAAAAGAATTTCATGTAAGAATTGTGCACATGAGACAAACTCCTGTAGAAAGAAAATTACCTTGAGCTAGAGAAATGAGAACTGGCTGAAATTCCTCTTTCTTATTCTCAGTGTTTGAATAATCAAAGCGGTCTTTAAATGTATAGGCGGGGCTGGGATAGCTCACCGCTTGTAATCCCACACTTTGCGAAGGCTGAGGCGGCGGATCATGAAGGGTCCAGGAGATCCGAGACCATCGGGCTTAACACCCGGTGAAACCCCCGTCTCTACTAAAAAGACAAAAAAGTAGCCGGGCGTTGTGGCGGGCAGCCTGTTAGTCCCAGCCGACTCGTGGAGGCTGAGATGGCAAAGAATGCGAGGAACCGGGAGGCGGAGCTTGCAGTGAGCGCGAATCGACCCCCCAGGGGACGCCACGGCACTCCAAGCCGTGGGCCGCGAGATGAGACTCAACGCCTCAAAAAAAAAAAAAAAAAAAAGTAAATATTTTCTTTTTGGGATAATGT
@amwenger
amwenger / in1.sam
Created January 6, 2015 01:20
Test case for samtools merge sort order validation
@HD VN:1.4 SO:coordinate
@SQ SN:1 LN:249250621
@RG ID:TEST PL:LS454 SM:TESTSM
A1 147 1 69584 0 101M = 69330 -355 ATGAGGTCGATAGTTTTTATTGTGACCTTCCTAGGGTAATCAAACTTGCCTGTACAGATACCTACAGGCTAGATATTATGGTCATTGCTAACAGTGGTGTG CA<DBDDBECAAB>DFDDFEHHHA@DGGGEGIIHHAEGIIIIHGGGGGECGGGFFGIF?CGGHDIJJIIHAIGIJIGJIJIIGEIIGIHHFGHFFFFFCCC NM:i:0 MD:Z:101 AS:i:101 XS:i:101 RG:Z:TEST
B1 99 1 69585 0 101M = 69759 275 TGAGGTCGATAGTTTTTATTGTGACCTTCCTAGGGTAATCAAACTTGCCTGTACAGATACCTACAGGCTAGATATTATGGTCATTGCTAACAGTGGTGTGC ?@@DD;DAACC@<CGHI=E4A:?492+AEF@FGDH9CA9*:DG3DA9*BDGI@DD8*....8BD=>@D@7@@=7ACC>ED7?)..;6;CC>@>>;A>@### NM:i:0 MD:Z:101 AS:i:101 XS:i:101 RG:Z:TEST
C1 83 1 69588 0 101M = 69571 -118 GGTCGATAGTTTTTATTGTGACCTTCCTAGGGTAATCAAACTTGCCTGTACAGATACCTACAGGCTAGATATTATGGTCATTGCTAACAGTGGTGTGCTCA ?;5=A>A:BCCCCCDB;DEC?;>E@;D9EC@HGC@GCIGGGGAF;CCFD9GHGHF?HFDGIHFC9GFC<F@CCHCGHDFC@IHE?<:FDFBHDDDDDD@?= NM:i:0 MD:Z:101 AS:i:101 XS:i:101 RG:Z:TEST
D1 163 1 69585 0 101M = 69629 145 TGAGGTCGATAGTTTTTATTGTGACCTTCCTAGGGTAATCAAACTTGCCTGTACAGATACCTACAG
@amwenger
amwenger / 65536.sam
Last active August 29, 2015 14:09
65,536 byte .sam file
@HD VN:1.4 SO:coordinate
@SQ SN:1 LN:249250621
@SQ SN:2 LN:243199373
@SQ SN:3 LN:198022430
@SQ SN:4 LN:191154276
@SQ SN:5 LN:180915260
@SQ SN:6 LN:171115067
@SQ SN:7 LN:159138663
@SQ SN:8 LN:146364022
@SQ SN:9 LN:141213431