How to get the SNP statistics for Hg19

Question

[MAPK]

I need to perform some mathematical analyses on human SNPs. I need information such as the number of SNPs in each chromosome, and also shared number of SNPs between different ethnicities etc. How can I obtain such information?

[Jorge Amigo]

maybe this particular data is already described in the literature. I usually query locally all 1000g's vcf files (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/) to get similar metrics. I find bcftools very helpful.

[MAPK]

Thank you, I will try this.

Answer 1

[Pierre Lindenbaum]

number of SNPs in each chromosomes

using ucsc / hg19

$ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -D hg19 -e 'select chrom,count(*) from  snp147 group by chrom' 
+-----------------------+----------+
| chrom                 | count(*) |
+-----------------------+----------+
| chr1                  | 11923447 |
| chr10                 |  7118919 |
| chr11                 |  7361809 |
| chr11_gl000202_random |       66 |
| chr12                 |  7060356 |
| chr13                 |  5018535 |
| chr14                 |  4787993 |
| chr15                 |  4423574 |
| chr16                 |  4993158 |
| chr17                 |  4456328 |
| chr17_ctg5_hap1       |    54172 |
| chr17_gl000203_random |      278 |
| chr17_gl000204_random |      162 |
| chr17_gl000205_random |     3903 |
| chr17_gl000206_random |       15 |
| chr18                 |  3984745 |
| chr18_gl000207_random |       62 |
| chr19                 |  3654726 |
| chr19_gl000208_random |     2215 |
| chr19_gl000209_random |      320 |
| chr1_gl000191_random  |       35 |
| chr1_gl000192_random  |      275 |
| chr2                  | 12691716 |
| chr20                 |  3361527 |
| chr21                 |  2016071 |
| chr21_gl000210_random |        4 |
| chr22                 |  2076346 |
| chr3                  | 10453846 |
| chr4                  | 10046674 |
| chr4_ctg9_hap1        |    34359 |
| chr4_gl000193_random  |     2989 |
| chr4_gl000194_random  |     3602 |
| chr5                  |  9362401 |
| chr6                  |  8975248 |
| chr6_apd_hap1         |   146264 |
| chr6_cox_hap2         |   312212 |
| chr6_dbb_hap3         |   269424 |
| chr6_mann_hap4        |   264315 |
| chr6_mcf_hap5         |   256896 |
| chr6_qbl_hap6         |   291958 |
| chr6_ssto_hap7        |   264812 |
| chr7                  |  8467782 |
| chr7_gl000195_random  |     6219 |
| chr8                  |  8105834 |
| chr8_gl000196_random  |        2 |
| chr8_gl000197_random  |        1 |
| chr9                  |  6487426 |
| chr9_gl000198_random  |     1995 |
| chr9_gl000199_random  |     2891 |
| chr9_gl000200_random  |       20 |
| chr9_gl000201_random  |       63 |
| chrM                  |     1579 |
| chrUn_gl000211        |     1536 |
| chrUn_gl000212        |     1793 |
| chrUn_gl000213        |       25 |
| chrUn_gl000214        |     1476 |
| chrUn_gl000215        |       33 |
| chrUn_gl000216        |      567 |
| chrUn_gl000217        |      165 |
| chrUn_gl000218        |     2879 |
| chrUn_gl000219        |     1911 |
| chrUn_gl000220        |     2556 |
| chrUn_gl000221        |     1223 |
| chrUn_gl000222        |      104 |
| chrUn_gl000223        |       12 |
| chrUn_gl000224        |     1793 |
| chrUn_gl000225        |     1437 |
| chrUn_gl000226        |      456 |
| chrUn_gl000227        |        6 |
| chrUn_gl000228        |       29 |
| chrUn_gl000229        |      124 |
| chrUn_gl000230        |      694 |
| chrUn_gl000231        |      171 |
| chrUn_gl000232        |      403 |
| chrUn_gl000233        |      511 |
| chrUn_gl000234        |      373 |
| chrUn_gl000235        |      198 |
| chrUn_gl000236        |        1 |
| chrUn_gl000237        |      140 |
| chrUn_gl000238        |       21 |
| chrUn_gl000239        |      135 |
| chrUn_gl000240        |      218 |
| chrUn_gl000241        |      164 |
| chrUn_gl000242        |        1 |
| chrUn_gl000243        |      128 |
| chrUn_gl000244        |        1 |
| chrUn_gl000245        |        7 |
| chrUn_gl000246        |        3 |
| chrUn_gl000247        |       36 |
| chrUn_gl000248        |        3 |
| chrUn_gl000249        |        1 |
| chrX                  |  5675522 |
| chrY                  |   375657 |
+-----------------------+----------+