diff --git a/.gitignore b/.gitignore index b91a2b1..3be7554 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,5 @@ # vendor / large data — never commit -data/ +/data/ refs/ _phase0_archive/ *.idat diff --git a/src/simurg/cn/data/cytoBand_GRCh37.txt.gz b/src/simurg/cn/data/cytoBand_GRCh37.txt.gz new file mode 100644 index 0000000..ee9ab76 Binary files /dev/null and b/src/simurg/cn/data/cytoBand_GRCh37.txt.gz differ diff --git a/src/simurg/cn/data/cytoBand_GRCh38.txt.gz b/src/simurg/cn/data/cytoBand_GRCh38.txt.gz new file mode 100644 index 0000000..691edde Binary files /dev/null and b/src/simurg/cn/data/cytoBand_GRCh38.txt.gz differ diff --git a/src/simurg/cn/data/mask_GRCh37.bed b/src/simurg/cn/data/mask_GRCh37.bed new file mode 100644 index 0000000..3504346 --- /dev/null +++ b/src/simurg/cn/data/mask_GRCh37.bed @@ -0,0 +1,26 @@ +# centromeres, gvar/stalk bands, acrocentric p-arms; derived from UCSC hg19 cytoBand +1 121500000 142600000 +2 90500000 96800000 +3 87900000 98300000 +4 48200000 52700000 +5 46100000 50700000 +6 58700000 63300000 +7 58000000 61700000 +8 43100000 48100000 +9 47300000 65900000 +10 38000000 42300000 +11 51600000 55700000 +12 33300000 38200000 +13 0 19500000 +14 0 19100000 +15 0 20700000 +16 34600000 47000000 +17 22200000 25800000 +18 15400000 19000000 +19 20000000 32400000 +20 25600000 29400000 +21 0 14300000 +22 0 17900000 +X 58100000 63000000 +Y 11600000 13400000 +Y 28800000 59373566 diff --git a/src/simurg/cn/data/mask_GRCh38.bed b/src/simurg/cn/data/mask_GRCh38.bed new file mode 100644 index 0000000..db1af68 --- /dev/null +++ b/src/simurg/cn/data/mask_GRCh38.bed @@ -0,0 +1,26 @@ +# centromeres, gvar/stalk bands, acrocentric p-arms; derived from UCSC hg38 cytoBand +1 121700000 143200000 +2 91800000 96000000 +3 87800000 98600000 +4 48200000 51800000 +5 46100000 51400000 +6 58500000 62600000 +7 58100000 62100000 +8 43200000 47200000 +9 42200000 61500000 +10 38000000 41600000 +11 51000000 55800000 +12 33200000 37800000 +13 0 18900000 +14 0 18200000 +15 0 20500000 +16 35300000 47000000 +17 22700000 27400000 +18 15400000 21500000 +19 19900000 31900000 +20 25700000 30400000 +21 0 13000000 +22 0 17400000 +X 58100000 63800000 +Y 10300000 10600000 +Y 26600000 57227415