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.