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Can you consider updating /bundle/2.8/b37/human_g1k_v37_decoy.fasta.fai.gz?

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Hi GATK team,

I found that using 'human_g1k_v37_decoy.fasta.fai' with samtools1.2 gives a floating point exception after a look at the fai indexes of human_g1k_v37_decoy.fasta.fai and human_g1k_v37.fasta.fai :

==> /apps/data//ftp.broadinstitute.org/bundle/2.8/b37//human_g1k_v37.fasta.fai <==
1   249250621   52  60  61
2   243199373   253404903   60  61
3   198022430   500657651   60  61
4   191154276   701980507   60  61
5   180915260   896320740   60  61
6   171115067   1080251307  60  61
7   159138663   1254218344  60  61
8   146364022   1416009371  60  61
9   141213431   1564812846  60  61
10  135534747   1708379889  60  61

==> /apps/data//ftp.broadinstitute.org/bundle/2.8/b37//human_g1k_v37_decoy.fasta.fai <==
1 dna:chromosome chromosome:GRCh37:1:1:249250621:1  249250621   52  60  61
2 dna:chromosome chromosome:GRCh37:2:1:243199373:1  243199373   253404903   60  61
3 dna:chromosome chromosome:GRCh37:3:1:198022430:1  198022430   500657651   60  61
4 dna:chromosome chromosome:GRCh37:4:1:191154276:1  191154276   701980507   60  61
5 dna:chromosome chromosome:GRCh37:5:1:180915260:1  180915260   896320740   60  61
6 dna:chromosome chromosome:GRCh37:6:1:171115067:1  171115067   1080251307  60  61
7 dna:chromosome chromosome:GRCh37:7:1:159138663:1  159138663   1254218344  60  61
8 dna:chromosome chromosome:GRCh37:8:1:146364022:1  146364022   1416009371  60  61
9 dna:chromosome chromosome:GRCh37:9:1:141213431:1  141213431   1564812846  60  61
10 dna:chromosome chromosome:GRCh37:10:1:135534747:1    135534747   1708379889  60  61

I concluded that Samtools cannot parse this header. This is fixable with samtools faidx human_g1k_v37_decoy.fasta. Consider updating the bundle to avoid confusion.

So can you update human_g1k_v37_decoy.fasta.fai.gz / human_g1k_v37_decoy.fasta.fai.gz.md5 ?


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