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yakneens/gist:dcc8f4a47753891cfa6c

Created October 13, 2015 20:31
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gistfile1.txt
[root@genotyper-8 centos]# zcat /reference/genome.fa.gz | grep chromosome
>1 dna:chromosome chromosome:GRCh37:1:1:249250621:1
>2 dna:chromosome chromosome:GRCh37:2:1:243199373:1
>3 dna:chromosome chromosome:GRCh37:3:1:198022430:1
>4 dna:chromosome chromosome:GRCh37:4:1:191154276:1
>5 dna:chromosome chromosome:GRCh37:5:1:180915260:1
>6 dna:chromosome chromosome:GRCh37:6:1:171115067:1
>7 dna:chromosome chromosome:GRCh37:7:1:159138663:1
>8 dna:chromosome chromosome:GRCh37:8:1:146364022:1
>9 dna:chromosome chromosome:GRCh37:9:1:141213431:1
>10 dna:chromosome chromosome:GRCh37:10:1:135534747:1
>11 dna:chromosome chromosome:GRCh37:11:1:135006516:1
>12 dna:chromosome chromosome:GRCh37:12:1:133851895:1
>13 dna:chromosome chromosome:GRCh37:13:1:115169878:1
>14 dna:chromosome chromosome:GRCh37:14:1:107349540:1
>15 dna:chromosome chromosome:GRCh37:15:1:102531392:1
>16 dna:chromosome chromosome:GRCh37:16:1:90354753:1
>17 dna:chromosome chromosome:GRCh37:17:1:81195210:1
>18 dna:chromosome chromosome:GRCh37:18:1:78077248:1
>19 dna:chromosome chromosome:GRCh37:19:1:59128983:1
>20 dna:chromosome chromosome:GRCh37:20:1:63025520:1
>21 dna:chromosome chromosome:GRCh37:21:1:48129895:1
>22 dna:chromosome chromosome:GRCh37:22:1:51304566:1
>X dna:chromosome chromosome:GRCh37:X:1:155270560:1
>Y dna:chromosome chromosome:GRCh37:Y:2649521:59034049:1
[root@genotyper-8 NA12878]# samtools view -H NA12878.chrom11.ILLUMINA.bwa.CEU.low_coverage.20121211.bam | more
@HD VN:1.0 SO:coordinate
@SQ SN:1 LN:249250621 M5:1b22b98cdeb4a9304cb5d48026a85128 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:2 LN:243199373 M5:a0d9851da00400dec1098a9255ac712e UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:3 LN:198022430 M5:fdfd811849cc2fadebc929bb925902e5 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:4 LN:191154276 M5:23dccd106897542ad87d2765d28a19a1 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:5 LN:180915260 M5:0740173db9ffd264d728f32784845cd7 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:6 LN:171115067 M5:1d3a93a248d92a729ee764823acbbc6b UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:7 LN:159138663 M5:618366e953d6aaad97dbe4777c29375e UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:8 LN:146364022 M5:96f514a9929e410c6651697bded59aec UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:9 LN:141213431 M5:3e273117f15e0a400f01055d9f393768 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:10 LN:135534747 M5:988c28e000e84c26d552359af1ea2e1d UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:11 LN:135006516 M5:98c59049a2df285c76ffb1c6db8f8b96 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:12 LN:133851895 M5:51851ac0e1a115847ad36449b0015864 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:13 LN:115169878 M5:283f8d7892baa81b510a015719ca7b0b UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:14 LN:107349540 M5:98f3cae32b2a2e9524bc19813927542e UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:15 LN:102531392 M5:e5645a794a8238215b2cd77acb95a078 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:16 LN:90354753 M5:fc9b1a7b42b97a864f56b348b06095e6 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:17 LN:81195210 M5:351f64d4f4f9ddd45b35336ad97aa6de UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:18 LN:78077248 M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:19 LN:59128983 M5:1aacd71f30db8e561810913e0b72636d UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:20 LN:63025520 M5:0dec9660ec1efaaf33281c0d5ea2560f UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:21 LN:48129895 M5:2979a6085bfe28e3ad6f552f361ed74d UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:22 LN:51304566 M5:a718acaa6135fdca8357d5bfe94211dd UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:X LN:155270560 M5:7e0e2e580297b7764e31dbc80c2540dd UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:Y LN:59373566 M5:1fa3474750af0948bdf97d5a0ee52e51 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:MT LN:16569 M5:c68f52674c9fb33aef52dcf399755519 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000207.1 LN:4262 M5:f3814841f1939d3ca19072d9e89f3fd7 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
[root@genotyper-8 reference]# md5sum genome.fa.gz
a07c7647c4f2e78977068e9a4a31af15 genome.fa.gz
[root@genotyper-8 reference]# md5sum hs37d5.fa.gz
a07c7647c4f2e78977068e9a4a31af15 hs37d5.fa.gz
[root@genotyper-8 reference]# samtools view -H /gnosdata/data/4023faaf-c73d-4587-a888-1c700fda100b/92a65acef03597a1e
00eff319bde3b44.bam | more
@HD VN:1.5 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
@SQ SN:10 LN:135534747
@SQ SN:11 LN:135006516
@SQ SN:12 LN:133851895
@SQ SN:13 LN:115169878
@SQ SN:14 LN:107349540
@SQ SN:15 LN:102531392
@SQ SN:16 LN:90354753
@SQ SN:17 LN:81195210
@SQ SN:18 LN:78077248
@SQ SN:19 LN:59128983
@SQ SN:20 LN:63025520
@SQ SN:21 LN:48129895
@SQ SN:22 LN:51304566
@SQ SN:X LN:155270560
@SQ SN:Y LN:59373566
@SQ SN:MT LN:16569
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